These are primarily sets of genes that I developed from multiple analyses on the genome.
This is a modification of this pipeline to include the updated HGT candidates.
#/work/GIF/remkv6/Baum/CamTechGenomeComparison/58_Renamatorium/26_ExpressionSets
library(GeneOverlap)
sed 's/\./\t/2' ../30_BenNewHGT/AllHGT.list |awk '{print $1}' >AllHGTRevised.list
sed 's/\./\t/2' ../30_BenNewHGT/HighConfHGT.list |awk '{print $1}' >HGTRevised.list
ls -1 *list|awk '{print $1" <- read.table(\""$1"\")"}' |less
x121EffectorOnlyNewGeneNames.list <- read.table("121EffectorOnlyNewGeneNames.list")
AllGenes.list <- read.table("AllGenes.list")
AllHGTRevised.list <- read.table("AllHGTRevised.list")
AllPredictedEffectorLTR.list <- read.table("AllPredictedEffectorLTR.list")
AllPredictedEffectorTIR.list <- read.table("AllPredictedEffectorTIR.list")
AllPredictedEffectorTandem.list <- read.table("AllPredictedEffectorTandem.list")
AllPredictedEffectors.list <- read.table("AllPredictedEffectors.list")
BuscoDNA.list <- read.table("BuscoDNA.list")
BuscoLTR.list <- read.table("BuscoLTR.list")
BuscoTandem.list <- read.table("BuscoTandem.list")
DorsalEffectorLTR.list <- read.table("DorsalEffectorLTR.list")
DorsalEffectorTIR.list <- read.table("DorsalEffectorTIR.list")
DorsalEffectorTandem.list <- read.table("DorsalEffectorTandem.list")
DorsallikeGenesFixed.list <- read.table("Dorsal-likeGenesFixed.list")
DuplicatedBuscosGene.list <- read.table("DuplicatedBuscosGene.list")
Family976.list <- read.table("Family976.list")
Family1265.list <- read.table("Family1265.list")
HGT.list <- read.table("HGT.list")
HGTNewNames.list <- read.table("HGTNewNames.list")
HGTRevised.list <- read.table("HGTRevised.list")
HighSNPDensity.list <- read.table("HighSNPDensity.list")
HighSNPDensity1Dev.list <- read.table("HighSNPDensity1Dev.list")
HighSNPDensity2Dev.list <- read.table("HighSNPDensity2Dev.list")
HighSNPDensity10Perc.list <- read.table("HighSNPDensity10Perc.list")
HighSignificant.list <- read.table("HighSignificant.list")
KnownEffectorLTR.list <- read.table("KnownEffectorLTR.list")
KnownEffectorTIR.list <- read.table("KnownEffectorTIR.list")
KnownEffectorTandem.list <- read.table("KnownEffectorTandem.list")
LowSignificant.list <- read.table("LowSignificant.list")
NonRedundantLtrRetroelementMerge.list <- read.table("NonRedundantLtrRetroelementMerge.list")
NotAllPredictedEffectorLTR.list <- read.table("NotAllPredictedEffectorLTR.list")
NotAllPredictedEffectorTIR.list <- read.table("NotAllPredictedEffectorTIR.list")
NotAllPredictedEffectorTandem.list <- read.table("NotAllPredictedEffectorTandem.list")
NotBuscoDNA.list <- read.table("NotBuscoDNA.list")
NotBuscoLTR.list <- read.table("NotBuscoLTR.list")
NotBuscoTandem.list <- read.table("NotBuscoTandem.list")
NotDorsalEffectorLTR.list <- read.table("NotDorsalEffectorLTR.list")
NotDorsalEffectorTIR.list <- read.table("NotDorsalEffectorTIR.list")
NotDorsalEffectorTandem.list <- read.table("NotDorsalEffectorTandem.list")
NotKnownEffectorLTR.list <- read.table("NotKnownEffectorLTR.list")
NotKnownEffectorTIR.list <- read.table("NotKnownEffectorTIR.list")
NotKnownEffectorTandem.list <- read.table("NotKnownEffectorTandem.list")
NotPredictedEffectorLTR.list <- read.table("NotPredictedEffectorLTR.list")
NotPredictedEffectorTIR.list <- read.table("NotPredictedEffectorTIR.list")
NotPredictedEffectorTandem.list <- read.table("NotPredictedEffectorTandem.list")
PredictedEffector.list <- read.table("PredictedEffector.list")
PredictedEffectorLTR.list <- read.table("PredictedEffectorLTR.list")
PredictedEffectorTIR.list <- read.table("PredictedEffectorTIR.list")
PredictedEffectorTandem.list <- read.table("PredictedEffectorTandem.list")
RepeatAffectedGenesNoSimple.list <- read.table("RepeatAffectedGenesNoSimple.list")
Secretome.gene.list <- read.table("Secretome.gene.list")
SupportedIRFMergeClassified.list <- read.table("SupportedIRFMergeClassified.list")
tandem.gene.list <- read.table("tandem.gene.list")
ls -1 *list |awk '{print "go.obj <- newGeneOverlap("$1"$V1, HighSignificant.list$V1, genome.size=All.genes)"}' |awk '{print $0"\ngo.obj"NR" <- testGeneOverlap(go.obj)"}' |less
Output of the above
##################################
go.obj <- newGeneOverlap(x121EffectorOnlyNewGeneNames.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj1 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllGenes.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj2 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllHGTRevised.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj3 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj4 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj5 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj6 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectors.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj7 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(BuscoDNA.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj8 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(BuscoLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj9 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(BuscoTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj10 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj11 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj12 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj13 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsallikeGenesFixed.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj14 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DuplicatedBuscosGene.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj15 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family976.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj16 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family1265.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj17 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGT.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj18 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTNewNames.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj19 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTRevised.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj20 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj21 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity1Dev.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj22 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity2Dev.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj23 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity10Perc.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj24 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSignificant.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj25 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj26 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj27 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj28 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(LowSignificant.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj29 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NonRedundantLtrRetroelementMerge.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj30 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj31 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj32 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj33 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotBuscoDNA.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj34 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotBuscoLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj35 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotBuscoTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj36 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj37 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj38 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj39 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj40 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj41 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj42 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj43 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj44 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj45 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffector.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj46 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorLTR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj47 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTIR.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj48 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTandem.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj49 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(RepeatAffectedGenesNoSimple.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj50 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Secretome.gene.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj51 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SupportedIRFMergeClassified.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj52 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(tandem.gene.list$V1, HighSignificant.list$V1, genome.size=All.genes)
go.obj53 <- testGeneOverlap(go.obj)
##################################
Last few commands to get the test Blast2go_finished
AllCombine <- c(go.obj1, go.obj2, go.obj3, go.obj4, go.obj5, go.obj6, go.obj7, go.obj8, go.obj9, go.obj10, go.obj11, go.obj12, go.obj13, go.obj14, go.obj15, go.obj16, go.obj17, go.obj18, go.obj19, go.obj20, go.obj21, go.obj22, go.obj23, go.obj24, go.obj25, go.obj26, go.obj27, go.obj28, go.obj29, go.obj30, go.obj31, go.obj32, go.obj33, go.obj34, go.obj35, go.obj36, go.obj37, go.obj38, go.obj39, go.obj40, go.obj41, go.obj42, go.obj43, go.obj44, go.obj45, go.obj46, go.obj47, go.obj48, go.obj49, go.obj50, go.obj51, go.obj52, go.obj53)
library(RJSONIO)
exportJSON <- toJSON(AllCombine)
write(exportJSON,"HighSignificant.out")
ls -1 *list |paste - <(less HighSignificant.out|sed 's/\[/\t/g' |awk 'NF<15' |grep "\"" | sed '0~5 s/$/\nwait/g' |tr "\n" "\t" |sed 's/wait/\n/g' |sed 's/,/\t/g' |sed 's/"//g' |cut -f 1-7,9- |sed 's/}//g') |less -S
121EffectorOnlyNewGeneNames.list notA: 28480 inA: 80 notA: 1170 inA: 41 ] pval: 7.3351e-27 Jaccard: 0.031758 is.tested: true
AllGenes.list notA: 28559 inA: 1 notA: 1211 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
AllHGTRevised.list notA: 27096 inA: 1464 notA: 1117 inA: 94 odds.ratio: 1.5575 pval: 8.9494e-05 Jaccard: 0.03514 is.tested: true
AllPredictedEffectorLTR.list notA: 28540 inA: 20 notA: 1209 inA: 2 odds.ratio: 2.3605 pval: 0.22477 Jaccard: 0.0016247 is.tested: true
AllPredictedEffectorTIR.list notA: 28510 inA: 50 notA: 1203 inA: 8 odds.ratio: 3.792 pval: 0.0023057 Jaccard: 0.0063442 is.tested: true
AllPredictedEffectorTandem.list notA: 28468 inA: 92 notA: 1187 inA: 24 odds.ratio: 6.2545 pval: 4.1118e-11 Jaccard: 0.018419 is.tested: true
AllPredictedEffectors.list notA: 28232 inA: 328 notA: 1108 inA: 103 odds.ratio: 8.001 pval: 1.2287e-49 Jaccard: 0.066927 is.tested: true
BuscoDNA.list notA: 28536 inA: 24 notA: 1211 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
BuscoLTR.list notA: 28540 inA: 20 notA: 1211 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
BuscoTandem.list notA: 28483 inA: 77 notA: 1209 inA: 2 odds.ratio: 0.61193 pval: 0.83681 Jaccard: 0.0015528 is.tested: true
DorsalEffectorLTR.list notA: 28555 inA: 5 notA: 1210 inA: 1 odds.ratio: 4.7193 pval: 0.22057 Jaccard: 0.00082237 is.tested: true
DorsalEffectorTIR.list notA: 28552 inA: 8 notA: 1204 inA: 7 odds.ratio: 20.743 pval: 8.746e-07 Jaccard: 0.0057424 is.tested: true
DorsalEffectorTandem.list notA: 28540 inA: 20 notA: 1193 inA: 18 odds.ratio: 21.523 pval: 1.2745e-15 Jaccard: 0.014622 is.tested: true
Dorsal-likeGenesFixed.list notA: 28471 inA: 89 notA: 1140 inA: 71 odds.ratio: 19.917 pval: 2.6556e-55 Jaccard: 0.054615 is.tested: true
DuplicatedBuscosGene.list notA: 28232 inA: 328 notA: 1196 inA: 15 odds.ratio: 1.0795 pval: 0.42433 Jaccard: 0.0097466 is.tested: true
Family976.list notA: 28473 inA: 87 notA: 1197 inA: 14 odds.ratio: 3.8278 pval: 5.9472e-05 Jaccard: 0.010786 is.tested: true
Family1265.list notA: 28451 inA: 109 notA: 1208 inA: 3 odds.ratio: 0.64823 pval: 0.83887 Jaccard: 0.0022727 is.tested: true
HGT.list notA: 27581 inA: 979 notA: 1177 inA: 34 odds.ratio: 0.81382 pval: 0.89653 Jaccard: 0.015525 is.tested: true
HGTNewNames.list notA: 28418 inA: 142 notA: 1206 inA: 5 odds.ratio: 0.82972 pval: 0.71839 Jaccard: 0.0036955 is.tested: true
HGTRevised.list notA: 28424 inA: 136 notA: 1196 inA: 15 odds.ratio: 2.6212 pval: 0.0013058 Jaccard: 0.011136 is.tested: true
HighSNPDensity.list notA: 28093 inA: 467 notA: 1184 inA: 27 odds.ratio: 1.3718 pval: 0.075161 Jaccard: 0.016091 is.tested: true
HighSNPDensity1Dev.list notA: 26682 inA: 1878 notA: 1111 inA: 100 odds.ratio: 1.2788 pval: 0.014393 Jaccard: 0.032373 is.tested: true
HighSNPDensity2Dev.list notA: 27728 inA: 832 notA: 1171 inA: 40 odds.ratio: 1.1384 pval: 0.23762 Jaccard: 0.019579 is.tested: true
HighSNPDensity10Perc.list notA: 25745 inA: 2815 notA: 1050 inA: 161 odds.ratio: 1.4023 pval: 0.00010255 Jaccard: 0.03999 is.tested: true
HighSignificant.list notA: 28560 inA: 0 notA: 0 inA: 1211 odds.ratio: Infinity pval: 0 Jaccard: 1 is.tested: true
KnownEffectorLTR.list notA: 28555 inA: 5 notA: 1211 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
KnownEffectorTIR.list notA: 28548 inA: 12 notA: 1206 inA: 5 odds.ratio: 9.8611 pval: 0.00045379 Jaccard: 0.0040883 is.tested: true
KnownEffectorTandem.list notA: 28531 inA: 29 notA: 1202 inA: 9 odds.ratio: 7.3639 pval: 1.66e-05 Jaccard: 0.0072581 is.tested: true
LowSignificant.list notA: 27992 inA: 568 notA: 1211 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
NonRedundantLtrRetroelementMerge.list notA: 27170 inA: 1390 notA: 1200 inA: 11 odds.ratio: 0.17918 pval: 1 Jaccard: 0.0042291 is.tested: true
NotAllPredictedEffectorLTR.list notA: 27190 inA: 1370 notA: 1202 inA: 9 odds.ratio: 0.14861 pval: 1 Jaccard: 0.003487 is.tested: true
NotAllPredictedEffectorTIR.list notA: 26732 inA: 1828 notA: 1182 inA: 29 odds.ratio: 0.35879 pval: 1 Jaccard: 0.0095426 is.tested: true
NotAllPredictedEffectorTandem.list notA: 22487 inA: 6073 notA: 1063 inA: 148 odds.ratio: 0.51556 pval: 1 Jaccard: 0.020319 is.tested: true
NotBuscoDNA.list notA: 26706 inA: 1854 notA: 1174 inA: 37 odds.ratio: 0.45398 pval: 1 Jaccard: 0.012072 is.tested: true
NotBuscoLTR.list notA: 27190 inA: 1370 notA: 1200 inA: 11 odds.ratio: 0.18193 pval: 1 Jaccard: 0.0042619 is.tested: true
NotBuscoTandem.list notA: 22472 inA: 6088 notA: 1041 inA: 170 odds.ratio: 0.60281 pval: 1 Jaccard: 0.023291 is.tested: true
NotDorsalEffectorLTR.list notA: 27175 inA: 1385 notA: 1201 inA: 10 odds.ratio: 0.16338 pval: 1 Jaccard: 0.0038521 is.tested: true
NotDorsalEffectorTIR.list notA: 26690 inA: 1870 notA: 1181 inA: 30 odds.ratio: 0.36257 pval: 1 Jaccard: 0.0097371 is.tested: true
NotDorsalEffectorTandem.list notA: 22415 inA: 6145 notA: 1057 inA: 154 odds.ratio: 0.53148 pval: 1 Jaccard: 0.020935 is.tested: true
NotKnownEffectorLTR.list notA: 27175 inA: 1385 notA: 1200 inA: 11 odds.ratio: 0.17986 pval: 1 Jaccard: 0.0042373 is.tested: true
NotKnownEffectorTIR.list notA: 26694 inA: 1866 notA: 1179 inA: 32 odds.ratio: 0.38828 pval: 1 Jaccard: 0.0104 is.tested: true
NotKnownEffectorTandem.list notA: 22424 inA: 6136 notA: 1048 inA: 163 odds.ratio: 0.56843 pval: 1 Jaccard: 0.022186 is.tested: true
NotPredictedEffectorLTR.list notA: 27187 inA: 1373 notA: 1202 inA: 9 odds.ratio: 0.14827 pval: 1 Jaccard: 0.003483 is.tested: true
NotPredictedEffectorTIR.list notA: 26728 inA: 1832 notA: 1180 inA: 31 odds.ratio: 0.38329 pval: 1 Jaccard: 0.010187 is.tested: true
NotPredictedEffectorTandem.list notA: 22471 inA: 6089 notA: 1053 inA: 158 odds.ratio: 0.55377 pval: 1 Jaccard: 0.021644 is.tested: true
PredictedEffector.list notA: 28322 inA: 238 notA: 1157 inA: 54 odds.ratio: 5.5533 pval: 7.2954e-21 Jaccard: 0.037267 is.tested: true
PredictedEffectorLTR.list notA: 28543 inA: 17 notA: 1209 inA: 2 odds.ratio: 2.7773 pval: 0.17969 Jaccard: 0.0016287 is.tested: true
PredictedEffectorTIR.list notA: 28514 inA: 46 notA: 1205 inA: 6 odds.ratio: 3.0863 pval: 0.018495 Jaccard: 0.0047733 is.tested: true
PredictedEffectorTandem.list notA: 28484 inA: 76 notA: 1197 inA: 14 odds.ratio: 4.3831 pval: 1.5865e-05 Jaccard: 0.010878 is.tested: true
RepeatAffectedGenesNoSimple.list notA: 16503 inA: 12057 notA: 911 inA: 300 odds.ratio: 0.45076 pval: 1 Jaccard: 0.022611 is.tested: true
Secretome.gene.list notA: 26685 inA: 1875 notA: 864 inA: 347 odds.ratio: 5.7144 pval: 6.9306e-115 Jaccard: 0.11244 is.tested: true
SupportedIRFMergeClassified.list notA: 26682 inA: 1878 notA: 1174 inA: 37 odds.ratio: 0.44778 pval: 1 Jaccard: 0.011978 is.tested: true
tandem.gene.list notA: 22395 inA: 6165 notA: 1039 inA: 172 odds.ratio: 0.60138 pval: 1 Jaccard: 0.023319 is.tested: true
go.obj <- newGeneOverlap(x121EffectorOnlyNewGeneNames.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj1 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllGenes.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj2 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllHGTRevised.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj3 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj4 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj5 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj6 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectors.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj7 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(BuscoDNA.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj8 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(BuscoLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj9 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(BuscoTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj10 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj11 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj12 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj13 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsallikeGenesFixed.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj14 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DuplicatedBuscosGene.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj15 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family976.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj16 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family1265.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj17 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGT.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj18 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTNewNames.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj19 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTRevised.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj20 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj21 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity1Dev.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj22 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity2Dev.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj23 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HighSNPDensity10Perc.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj24 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(LowSignificant.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj25 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj26 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj27 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj28 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(LowSignificant.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj29 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NonRedundantLtrRetroelementMerge.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj30 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj31 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj32 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj33 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotBuscoDNA.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj34 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotBuscoLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj35 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotBuscoTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj36 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj37 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj38 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj39 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj40 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj41 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj42 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj43 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj44 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj45 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffector.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj46 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorLTR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj47 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTIR.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj48 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTandem.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj49 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(RepeatAffectedGenesNoSimple.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj50 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Secretome.gene.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj51 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SupportedIRFMergeClassified.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj52 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(tandem.gene.list$V1, LowSignificant.list$V1, genome.size=All.genes)
go.obj53 <- testGeneOverlap(go.obj)
Last few commands to get the chart
AllCombine <- c(go.obj1, go.obj2, go.obj3, go.obj4, go.obj5, go.obj6, go.obj7, go.obj8, go.obj9, go.obj10, go.obj11, go.obj12, go.obj13, go.obj14, go.obj15, go.obj16, go.obj17, go.obj18, go.obj19, go.obj20, go.obj21, go.obj22, go.obj23, go.obj24, go.obj25, go.obj26, go.obj27, go.obj28, go.obj29, go.obj30, go.obj31, go.obj32, go.obj33, go.obj34, go.obj35, go.obj36, go.obj37, go.obj38, go.obj39, go.obj40, go.obj41, go.obj42, go.obj43, go.obj44, go.obj45, go.obj46, go.obj47, go.obj48, go.obj49, go.obj50, go.obj51, go.obj52, go.obj53)
library(RJSONIO)
exportJSON <- toJSON(AllCombine)
write(exportJSON,"LowSignificant.out")
#format the file so it is a readable table
ls -1 *list |paste - <(less LowSignificant.out|sed 's/\[/\t/g' |awk 'NF<15' |grep "\"" | sed '0~5 s/$/\nwait/g' |tr "\n" "\t" |sed 's/wait/\n/g' |sed 's/,/\t/g' |sed 's/"//g' |cut -f 1-7,9- |sed 's/}//g') |less -S
121EffectorOnlyNewGeneNames.list notA: 29093 inA: 110 notA: 557 inA: 11 ] pval: 2.1312e-05 Jaccard: 0.016224 is.tested: true
AllGenes.list notA: 29202 inA: 1 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
AllHGTRevised.list notA: 27678 inA: 1525 notA: 535 inA: 33 odds.ratio: 1.1195 pval: 0.29201 Jaccard: 0.015767 is.tested: true
AllPredictedEffectorLTR.list notA: 29181 inA: 22 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
AllPredictedEffectorTIR.list notA: 29147 inA: 56 notA: 566 inA: 2 odds.ratio: 1.8392 pval: 0.30378 Jaccard: 0.0032051 is.tested: true
AllPredictedEffectorTandem.list notA: 29095 inA: 108 notA: 560 inA: 8 odds.ratio: 3.8483 pval: 0.001754 Jaccard: 0.011834 is.tested: true
AllPredictedEffectors.list notA: 28793 inA: 410 notA: 547 inA: 21 odds.ratio: 2.6958 pval: 9.7619e-05 Jaccard: 0.021472 is.tested: true
BuscoDNA.list notA: 29179 inA: 24 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
BuscoLTR.list notA: 29183 inA: 20 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
BuscoTandem.list notA: 29126 inA: 77 notA: 566 inA: 2 odds.ratio: 1.3366 pval: 0.44644 Jaccard: 0.0031008 is.tested: true
DorsalEffectorLTR.list notA: 29197 inA: 6 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
DorsalEffectorTIR.list notA: 29190 inA: 13 notA: 566 inA: 2 odds.ratio: 7.9331 pval: 0.032376 Jaccard: 0.0034423 is.tested: true
DorsalEffectorTandem.list notA: 29170 inA: 33 notA: 563 inA: 5 odds.ratio: 7.8493 pval: 0.00074105 Jaccard: 0.0083195 is.tested: true
Dorsal-likeGenesFixed.list notA: 29056 inA: 147 notA: 555 inA: 13 odds.ratio: 4.6295 pval: 1.3198e-05 Jaccard: 0.018182 is.tested: true
DuplicatedBuscosGene.list notA: 28868 inA: 335 notA: 560 inA: 8 odds.ratio: 1.231 pval: 0.33264 Jaccard: 0.0088594 is.tested: true
Family976.list notA: 29105 inA: 98 notA: 565 inA: 3 odds.ratio: 1.5769 pval: 0.30332 Jaccard: 0.0045045 is.tested: true
Family1265.list notA: 29091 inA: 112 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
HGT.list notA: 28207 inA: 996 notA: 551 inA: 17 odds.ratio: 0.87377 pval: 0.73913 Jaccard: 0.01087 is.tested: true
HGTNewNames.list notA: 29059 inA: 144 notA: 565 inA: 3 odds.ratio: 1.0715 pval: 0.53396 Jaccard: 0.0042135 is.tested: true
HGTRevised.list notA: 29061 inA: 142 notA: 559 inA: 9 odds.ratio: 3.2947 pval: 0.002538 Jaccard: 0.012676 is.tested: true
HighSNPDensity.list notA: 28717 inA: 486 notA: 560 inA: 8 odds.ratio: 0.84412 pval: 0.7281 Jaccard: 0.0075901 is.tested: true
HighSNPDensity1Dev.list notA: 27267 inA: 1936 notA: 526 inA: 42 odds.ratio: 1.1246 pval: 0.25659 Jaccard: 0.016773 is.tested: true
HighSNPDensity2Dev.list notA: 28350 inA: 853 notA: 549 inA: 19 odds.ratio: 1.1502 pval: 0.30939 Jaccard: 0.013371 is.tested: true
HighSNPDensity10Perc.list notA: 26290 inA: 2913 notA: 505 inA: 63 odds.ratio: 1.1259 pval: 0.20769 Jaccard: 0.018098 is.tested: true
HighSignificant.list notA: 29203 inA: 0 notA: 0 inA: 568 odds.ratio: Infinity pval: 0 Jaccard: 1 is.tested: true
KnownEffectorLTR.list notA: 29198 inA: 5 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
KnownEffectorTIR.list notA: 29187 inA: 16 notA: 567 inA: 1 odds.ratio: 3.217 pval: 0.27932 Jaccard: 0.0017123 is.tested: true
KnownEffectorTandem.list notA: 29170 inA: 33 notA: 563 inA: 5 odds.ratio: 7.8493 pval: 0.00074105 Jaccard: 0.0083195 is.tested: true
LowSignificant.list notA: 29203 inA: 0 notA: 0 inA: 568 odds.ratio: Infinity pval: 0 Jaccard: 1 is.tested: true
NonRedundantLtrRetroelementMerge.list notA: 27809 inA: 1394 notA: 561 inA: 7 odds.ratio: 0.24893 pval: 1 Jaccard: 0.0035678 is.tested: true
NotAllPredictedEffectorLTR.list notA: 27831 inA: 1372 notA: 561 inA: 7 odds.ratio: 0.25312 pval: 1 Jaccard: 0.0036082 is.tested: true
NotAllPredictedEffectorTIR.list notA: 27362 inA: 1841 notA: 552 inA: 16 odds.ratio: 0.43081 pval: 0.99995 Jaccard: 0.0066418 is.tested: true
NotAllPredictedEffectorTandem.list notA: 23025 inA: 6178 notA: 525 inA: 43 odds.ratio: 0.30526 pval: 1 Jaccard: 0.0063741 is.tested: true
NotBuscoDNA.list notA: 27330 inA: 1873 notA: 550 inA: 18 odds.ratio: 0.47755 pval: 0.99979 Jaccard: 0.007374 is.tested: true
NotBuscoLTR.list notA: 27829 inA: 1374 notA: 561 inA: 7 odds.ratio: 0.25273 pval: 1 Jaccard: 0.0036045 is.tested: true
NotBuscoTandem.list notA: 22994 inA: 6209 notA: 519 inA: 49 odds.ratio: 0.34964 pval: 1 Jaccard: 0.0072303 is.tested: true
NotDorsalEffectorLTR.list notA: 27815 inA: 1388 notA: 561 inA: 7 odds.ratio: 0.25006 pval: 1 Jaccard: 0.0035787 is.tested: true
NotDorsalEffectorTIR.list notA: 27319 inA: 1884 notA: 552 inA: 16 odds.ratio: 0.42031 pval: 0.99997 Jaccard: 0.0065253 is.tested: true
NotDorsalEffectorTandem.list notA: 22950 inA: 6253 notA: 522 inA: 46 odds.ratio: 0.32343 pval: 1 Jaccard: 0.0067439 is.tested: true
NotKnownEffectorLTR.list notA: 27814 inA: 1389 notA: 561 inA: 7 odds.ratio: 0.24987 pval: 1 Jaccard: 0.0035769 is.tested: true
NotKnownEffectorTIR.list notA: 27322 inA: 1881 notA: 551 inA: 17 odds.ratio: 0.44816 pval: 0.99992 Jaccard: 0.0069416 is.tested: true
NotKnownEffectorTandem.list notA: 22950 inA: 6253 notA: 522 inA: 46 odds.ratio: 0.32343 pval: 1 Jaccard: 0.0067439 is.tested: true
NotPredictedEffectorLTR.list notA: 27828 inA: 1375 notA: 561 inA: 7 odds.ratio: 0.25254 pval: 1 Jaccard: 0.0036027 is.tested: true
NotPredictedEffectorTIR.list notA: 27357 inA: 1846 notA: 551 inA: 17 odds.ratio: 0.45724 pval: 0.99988 Jaccard: 0.0070423 is.tested: true
NotPredictedEffectorTandem.list notA: 23001 inA: 6202 notA: 523 inA: 45 odds.ratio: 0.3191 pval: 1 Jaccard: 0.006647 is.tested: true
PredictedEffector.list notA: 28918 inA: 285 notA: 561 inA: 7 odds.ratio: 1.2661 pval: 0.32415 Jaccard: 0.0082063 is.tested: true
PredictedEffectorLTR.list notA: 29184 inA: 19 notA: 568 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
PredictedEffectorTIR.list notA: 29152 inA: 51 notA: 567 inA: 1 odds.ratio: 1.0081 pval: 0.63306 Jaccard: 0.0016155 is.tested: true
PredictedEffectorTandem.list notA: 29119 inA: 84 notA: 562 inA: 6 odds.ratio: 3.7009 pval: 0.0075792 Jaccard: 0.0092025 is.tested: true
RepeatAffectedGenesNoSimple.list notA: 16989 inA: 12214 notA: 425 inA: 143 odds.ratio: 0.46803 pval: 1 Jaccard: 0.011188 is.tested: true
Secretome.gene.list notA: 27081 inA: 2122 notA: 468 inA: 100 odds.ratio: 2.7267 pval: 6.4594e-16 Jaccard: 0.037175 is.tested: true
SupportedIRFMergeClassified.list notA: 27306 inA: 1897 notA: 550 inA: 18 odds.ratio: 0.4711 pval: 0.99984 Jaccard: 0.0073022 is.tested: true
tandem.gene.list notA: 22917 inA: 6286 notA: 517 inA: 51 odds.ratio: 0.35964 pval: 1 Jaccard: 0.0074409 is.tested: true
#/work/GIF/remkv6/Baum/CamTechGenomeComparison/58_Renamatorium/28_SNPDensity
sed 's/\./\t/2' ../30_BenNewHGT/AllHGT.list |awk '{print $1}' >AllHGTRevised.list
sed 's/\./\t/2' ../30_BenNewHGT/HighConfHGT.list |awk '{print $1}' >HGTRevised.list
ls -1 *list|awk '{print $1" <- read.table(\""$1"\")"}' |less
###############################################
x121EffectorOnlyNewGeneNames.list <- read.table("121EffectorOnlyNewGeneNames.list")
AllGenes.list <- read.table("AllGenes.list")
AllHGTRevised.list <- read.table("AllHGTRevised.list")
AllPredictedEffectorLTR.list <- read.table("AllPredictedEffectorLTR.list")
AllPredictedEffectorTIR.list <- read.table("AllPredictedEffectorTIR.list")
AllPredictedEffectorTandem.list <- read.table("AllPredictedEffectorTandem.list")
AllPredictedEffectors.list <- read.table("AllPredictedEffectors.list")
DorsalEffectorLTR.list <- read.table("DorsalEffectorLTR.list")
DorsalEffectorTIR.list <- read.table("DorsalEffectorTIR.list")
DorsalEffectorTandem.list <- read.table("DorsalEffectorTandem.list")
DorsallikeGenesFixed.list <- read.table("Dorsal-likeGenesFixed.list")
Family976.list <- read.table("Family976.list")
Family1265.list <- read.table("Family1265.list")
HGT.list <- read.table("HGT.list")
HGTNewNames.list <- read.table("HGTNewNames.list")
HGTRevised.list <- read.table("HGTRevised.list")
KnownEffectorLTR.list <- read.table("KnownEffectorLTR.list")
KnownEffectorTIR.list <- read.table("KnownEffectorTIR.list")
KnownEffectorTandem.list <- read.table("KnownEffectorTandem.list")
NonRedundantLtrRetroelementMerge.list <- read.table("NonRedundantLtrRetroelementMerge.list")
NotAllPredictedEffectorLTR.list <- read.table("NotAllPredictedEffectorLTR.list")
NotAllPredictedEffectorTIR.list <- read.table("NotAllPredictedEffectorTIR.list")
NotAllPredictedEffectorTandem.list <- read.table("NotAllPredictedEffectorTandem.list")
NotDorsalEffectorLTR.list <- read.table("NotDorsalEffectorLTR.list")
NotDorsalEffectorTIR.list <- read.table("NotDorsalEffectorTIR.list")
NotDorsalEffectorTandem.list <- read.table("NotDorsalEffectorTandem.list")
NotKnownEffectorLTR.list <- read.table("NotKnownEffectorLTR.list")
NotKnownEffectorTIR.list <- read.table("NotKnownEffectorTIR.list")
NotKnownEffectorTandem.list <- read.table("NotKnownEffectorTandem.list")
NotPredictedEffectorLTR.list <- read.table("NotPredictedEffectorLTR.list")
NotPredictedEffectorTIR.list <- read.table("NotPredictedEffectorTIR.list")
NotPredictedEffectorTandem.list <- read.table("NotPredictedEffectorTandem.list")
PredictedEffector.list <- read.table("PredictedEffector.list")
PredictedEffectorLTR.list <- read.table("PredictedEffectorLTR.list")
PredictedEffectorTIR.list <- read.table("PredictedEffectorTIR.list")
PredictedEffectorTandem.list <- read.table("PredictedEffectorTandem.list")
RepeatAffectedGenesNoSimple.list <- read.table("RepeatAffectedGenesNoSimple.list")
SNPDensityAll0SNPS.list <- read.table("SNPDensityAll0SNPS.list")
SNPDensityAll10Percentile.list <- read.table("SNPDensityAll10Percentile.list")
SNPDensityAll10percAfterRemoveZeros.list <- read.table("SNPDensityAll10percAfterRemoveZeros.list")
SNPDensityAll90Percentile.list <- read.table("SNPDensityAll90Percentile.list")
Secretome.gene.list <- read.table("Secretome.gene.list")
SupportedIRFMergeClassified.list <- read.table("SupportedIRFMergeClassified.list")
tandem.gene.list <- read.table("tandem.gene.list")
###############################################
ls -1 *list |awk '{print "go.obj <- newGeneOverlap("$1"$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)"}' |awk '{print $0"\ngo.obj"NR" <- testGeneOverlap(go.obj)"}' |less
#################################################
go.obj <- newGeneOverlap(x121EffectorOnlyNewGeneNames.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj1 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllGenes.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj2 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllHGTRevised.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj3 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj4 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj5 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj6 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectors.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj7 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj8 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj9 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj10 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsallikeGenesFixed.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj11 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family976.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj12 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family1265.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj13 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGT.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj14 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTNewNames.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj15 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTRevised.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj16 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj17 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj18 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj19 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NonRedundantLtrRetroelementMerge.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj20 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj21 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj22 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj23 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj24 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj25 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj26 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj27 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj28 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj29 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj30 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj31 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj32 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffector.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj33 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorLTR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj34 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTIR.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj35 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTandem.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj36 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(RepeatAffectedGenesNoSimple.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj37 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll0SNPS.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj38 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll10Percentile.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj39 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll10percAfterRemoveZeros.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj40 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll90Percentile.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj41 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Secretome.gene.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj42 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SupportedIRFMergeClassified.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj43 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(tandem.gene.list$V1, SNPDensityAll10percAfterRemoveZeros.list$V1, genome.size=All.genes)
go.obj44 <- testGeneOverlap(go.obj)
#################################################
#last few commands to perform the tested
AllCombine <- c(go.obj1, go.obj2, go.obj3, go.obj4, go.obj5, go.obj6, go.obj7, go.obj8, go.obj9, go.obj10, go.obj11, go.obj12, go.obj13, go.obj14, go.obj15, go.obj16, go.obj17, go.obj18, go.obj19, go.obj20, go.obj21, go.obj22, go.obj23, go.obj24, go.obj25, go.obj26, go.obj27, go.obj28, go.obj29, go.obj30, go.obj31, go.obj32, go.obj33, go.obj34, go.obj35, go.obj36, go.obj37, go.obj38, go.obj39, go.obj40, go.obj41, go.obj42, go.obj43, go.obj44)
library(RJSONIO)
exportJSON <- toJSON(AllCombine)
write(exportJSON,"SNPDensityAll10percAfterRemoveZeros.out")
ls -1 *list |paste - <(less SNPDensityAll10percAfterRemoveZeros.out|sed 's/\[/\t/g' |awk 'NF<15' |grep "\"" | sed '0~5 s/$/\nwait/g' |tr "\n" "\t" |sed 's/wait/\n/g' |sed 's/,/\t/g' |sed 's/"//g' |cut -f 1-7,9- |sed 's/}//g') |less -S
121EffectorOnlyNewGeneNames.list notA: 27138 inA: 117 notA: 2512 inA: 4 ] pval: 0.99319 Jaccard: 0.0015192 is.tested: true
AllGenes.list notA: 27254 inA: 1 notA: 2516 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
AllHGTRevised.list notA: 25866 inA: 1389 notA: 2347 inA: 169 odds.ratio: 1.3409 pval: 0.00042846 Jaccard: 0.043278 is.tested: true
AllPredictedEffectorLTR.list notA: 27238 inA: 17 notA: 2511 inA: 5 odds.ratio: 3.1902 pval: 0.033545 Jaccard: 0.0019739 is.tested: true
AllPredictedEffectorTIR.list notA: 27205 inA: 50 notA: 2508 inA: 8 odds.ratio: 1.7355 pval: 0.11367 Jaccard: 0.0031177 is.tested: true
AllPredictedEffectorTandem.list notA: 27151 inA: 104 notA: 2504 inA: 12 odds.ratio: 1.2511 pval: 0.27473 Jaccard: 0.0045802 is.tested: true
AllPredictedEffectors.list notA: 26859 inA: 396 notA: 2481 inA: 35 odds.ratio: 0.95683 pval: 0.62347 Jaccard: 0.012019 is.tested: true
DorsalEffectorLTR.list notA: 27251 inA: 4 notA: 2514 inA: 2 odds.ratio: 5.4188 pval: 0.085166 Jaccard: 0.00079365 is.tested: true
DorsalEffectorTIR.list notA: 27240 inA: 15 notA: 2516 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
DorsalEffectorTandem.list notA: 27221 inA: 34 notA: 2512 inA: 4 odds.ratio: 1.2749 pval: 0.40203 Jaccard: 0.0015686 is.tested: true
Dorsal-likeGenesFixed.list notA: 27107 inA: 148 notA: 2504 inA: 12 odds.ratio: 0.87774 pval: 0.70861 Jaccard: 0.0045045 is.tested: true
Family976.list notA: 27160 inA: 95 notA: 2510 inA: 6 odds.ratio: 0.68345 pval: 0.86488 Jaccard: 0.002298 is.tested: true
Family1265.list notA: 27152 inA: 103 notA: 2507 inA: 9 odds.ratio: 0.94635 pval: 0.6123 Jaccard: 0.0034364 is.tested: true
HGT.list notA: 26319 inA: 936 notA: 2439 inA: 77 odds.ratio: 0.8877 pval: 0.85289 Jaccard: 0.022306 is.tested: true
HGTNewNames.list notA: 27120 inA: 135 notA: 2504 inA: 12 odds.ratio: 0.96273 pval: 0.59319 Jaccard: 0.0045266 is.tested: true
HGTRevised.list notA: 27120 inA: 135 notA: 2500 inA: 16 odds.ratio: 1.2857 pval: 0.20657 Jaccard: 0.0060355 is.tested: true
KnownEffectorLTR.list notA: 27250 inA: 5 notA: 2516 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
KnownEffectorTIR.list notA: 27240 inA: 15 notA: 2514 inA: 2 odds.ratio: 1.4447 pval: 0.42735 Jaccard: 0.0007902 is.tested: true
KnownEffectorTandem.list notA: 27220 inA: 35 notA: 2513 inA: 3 odds.ratio: 0.92843 pval: 0.63377 Jaccard: 0.001176 is.tested: true
NonRedundantLtrRetroelementMerge.list notA: 25977 inA: 1278 notA: 2393 inA: 123 odds.ratio: 1.0448 pval: 0.33958 Jaccard: 0.03242 is.tested: true
NotAllPredictedEffectorLTR.list notA: 25994 inA: 1261 notA: 2398 inA: 118 odds.ratio: 1.0144 pval: 0.45726 Jaccard: 0.031242 is.tested: true
NotAllPredictedEffectorTIR.list notA: 25568 inA: 1687 notA: 2346 inA: 170 odds.ratio: 1.0982 pval: 0.13991 Jaccard: 0.040447 is.tested: true
NotAllPredictedEffectorTandem.list notA: 21618 inA: 5637 notA: 1932 inA: 584 odds.ratio: 1.1592 pval: 0.001698 Jaccard: 0.07163 is.tested: true
NotDorsalEffectorLTR.list notA: 25981 inA: 1274 notA: 2395 inA: 121 odds.ratio: 1.0303 pval: 0.39417 Jaccard: 0.031926 is.tested: true
NotDorsalEffectorTIR.list notA: 25533 inA: 1722 notA: 2338 inA: 178 odds.ratio: 1.1288 pval: 0.075997 Jaccard: 0.042001 is.tested: true
NotDorsalEffectorTandem.list notA: 21548 inA: 5707 notA: 1924 inA: 592 odds.ratio: 1.1617 pval: 0.0014094 Jaccard: 0.071993 is.tested: true
NotKnownEffectorLTR.list notA: 25982 inA: 1273 notA: 2393 inA: 123 odds.ratio: 1.0491 pval: 0.32437 Jaccard: 0.032462 is.tested: true
NotKnownEffectorTIR.list notA: 25533 inA: 1722 notA: 2340 inA: 176 odds.ratio: 1.1152 pval: 0.10006 Jaccard: 0.041529 is.tested: true
NotKnownEffectorTandem.list notA: 21549 inA: 5706 notA: 1923 inA: 593 odds.ratio: 1.1645 pval: 0.001196 Jaccard: 0.072124 is.tested: true
NotPredictedEffectorLTR.list notA: 25993 inA: 1262 notA: 2396 inA: 120 odds.ratio: 1.0316 pval: 0.38998 Jaccard: 0.031763 is.tested: true
NotPredictedEffectorTIR.list notA: 25562 inA: 1693 notA: 2346 inA: 170 odds.ratio: 1.0941 pval: 0.15 Jaccard: 0.04039 is.tested: true
NotPredictedEffectorTandem.list notA: 21597 inA: 5658 notA: 1927 inA: 589 odds.ratio: 1.1667 pval: 0.0010875 Jaccard: 0.072058 is.tested: true
PredictedEffector.list notA: 26985 inA: 270 notA: 2494 inA: 22 odds.ratio: 0.88162 pval: 0.74404 Jaccard: 0.0078966 is.tested: true
PredictedEffectorLTR.list notA: 27239 inA: 16 notA: 2513 inA: 3 odds.ratio: 2.0323 pval: 0.21327 Jaccard: 0.0011848 is.tested: true
PredictedEffectorTIR.list notA: 27211 inA: 44 notA: 2508 inA: 8 odds.ratio: 1.9726 pval: 0.069072 Jaccard: 0.003125 is.tested: true
PredictedEffectorTandem.list notA: 27172 inA: 83 notA: 2509 inA: 7 odds.ratio: 0.91336 pval: 0.64605 Jaccard: 0.0026933 is.tested: true
RepeatAffectedGenesNoSimple.list notA: 15733 inA: 11522 notA: 1681 inA: 835 odds.ratio: 0.67828 pval: 1 Jaccard: 0.059481 is.tested: true
SNPDensityAll0SNPS.list notA: 22643 inA: 4612 notA: 2516 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
SNPDensityAll10Percentile.list notA: 24285 inA: 2970 notA: 2516 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
SNPDensityAll10percAfterRemoveZeros.list notA: 27255 inA: 0 notA: 0 inA: 2516 odds.ratio: Infinity pval: 0 Jaccard: 1 is.tested: true
SNPDensityAll90Percentile.list notA: 24286 inA: 2969 notA: 2516 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
Secretome.gene.list notA: 25189 inA: 2066 notA: 2360 inA: 156 odds.ratio: 0.80593 pval: 0.99556 Jaccard: 0.034046 is.tested: true
SupportedIRFMergeClassified.list notA: 25518 inA: 1737 notA: 2338 inA: 178 odds.ratio: 1.1184 pval: 0.092974 Jaccard: 0.041853 is.tested: true
tandem.gene.list notA: 21514 inA: 5741 notA: 1920 inA: 596 odds.ratio: 1.1632 pval: 0.0012647 Jaccard: 0.072181 is.tested: true
ls -1 *list |awk '{print "go.obj <- newGeneOverlap("$1"$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)"}' |awk '{print $0"\ngo.obj"NR" <- testGeneOverlap(go.obj)"}' |less
go.obj <- newGeneOverlap(x121EffectorOnlyNewGeneNames.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj1 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllGenes.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj2 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllHGTRevised.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj3 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj4 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj5 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj6 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectors.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj7 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj8 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj9 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj10 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsallikeGenesFixed.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj11 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family976.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj12 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family1265.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj13 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGT.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj14 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTNewNames.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj15 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTRevised.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj16 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj17 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj18 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj19 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NonRedundantLtrRetroelementMerge.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj20 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj21 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj22 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj23 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj24 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj25 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj26 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj27 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj28 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj29 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj30 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj31 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj32 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffector.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj33 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorLTR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj34 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTIR.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj35 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTandem.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj36 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(RepeatAffectedGenesNoSimple.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj37 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll0SNPS.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj38 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll10Percentile.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj39 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll10percAfterRemoveZeros.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj40 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll90Percentile.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj41 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Secretome.gene.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj42 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SupportedIRFMergeClassified.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj43 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(tandem.gene.list$V1, SNPDensityAll90Percentile.list$V1, genome.size=All.genes)
go.obj44 <- testGeneOverlap(go.obj)
###############################################
#commands that perform the test
AllCombine <- c(go.obj1, go.obj2, go.obj3, go.obj4, go.obj5, go.obj6, go.obj7, go.obj8, go.obj9, go.obj10, go.obj11, go.obj12, go.obj13, go.obj14, go.obj15, go.obj16, go.obj17, go.obj18, go.obj19, go.obj20, go.obj21, go.obj22, go.obj23, go.obj24, go.obj25, go.obj26, go.obj27, go.obj28, go.obj29, go.obj30, go.obj31, go.obj32, go.obj33, go.obj34, go.obj35, go.obj36, go.obj37, go.obj38, go.obj39, go.obj40, go.obj41, go.obj42, go.obj43, go.obj44)
library(RJSONIO)
exportJSON <- toJSON(AllCombine)
write(exportJSON,"SNPDensityAll90Percentile.out")
#take the results and reformat into a table.
ls -1 *list |paste - <(less SNPDensityAll90Percentile.out|sed 's/\[/\t/g' |awk 'NF<15' |grep "\"" | sed '0~5 s/$/\nwait/g' |tr "\n" "\t" |sed 's/wait/\n/g' |sed 's/,/\t/g' |sed 's/"//g' |cut -f 1-7,9- |sed 's/}//g') |less -S
121EffectorOnlyNewGeneNames.list notA: 26698 inA: 104 notA: 2952 inA: 17 ] pval: 0.093069 Jaccard: 0.0055321 is.tested: true
AllGenes.list notA: 26801 inA: 1 notA: 2969 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
AllHGTRevised.list notA: 25389 inA: 1413 notA: 2824 inA: 145 odds.ratio: 0.92258 pval: 0.82732 Jaccard: 0.03309 is.tested: true
AllPredictedEffectorLTR.list notA: 26781 inA: 21 notA: 2968 inA: 1 odds.ratio: 0.42969 pval: 0.90095 Jaccard: 0.00033445 is.tested: true
AllPredictedEffectorTIR.list notA: 26751 inA: 51 notA: 2962 inA: 7 odds.ratio: 1.2396 pval: 0.35702 Jaccard: 0.0023179 is.tested: true
AllPredictedEffectorTandem.list notA: 26700 inA: 102 notA: 2955 inA: 14 odds.ratio: 1.2402 pval: 0.26566 Jaccard: 0.0045588 is.tested: true
AllPredictedEffectors.list notA: 26411 inA: 391 notA: 2929 inA: 40 odds.ratio: 0.92246 pval: 0.70865 Jaccard: 0.011905 is.tested: true
DorsalEffectorLTR.list notA: 26796 inA: 6 notA: 2969 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
DorsalEffectorTIR.list notA: 26790 inA: 12 notA: 2966 inA: 3 odds.ratio: 2.258 pval: 0.18297 Jaccard: 0.0010064 is.tested: true
DorsalEffectorTandem.list notA: 26771 inA: 31 notA: 2962 inA: 7 odds.ratio: 2.0408 pval: 0.078911 Jaccard: 0.0023333 is.tested: true
Dorsal-likeGenesFixed.list notA: 26660 inA: 142 notA: 2951 inA: 18 odds.ratio: 1.1452 pval: 0.33097 Jaccard: 0.0057859 is.tested: true
Family976.list notA: 26711 inA: 91 notA: 2959 inA: 10 odds.ratio: 0.99198 pval: 0.55838 Jaccard: 0.003268 is.tested: true
Family1265.list notA: 26698 inA: 104 notA: 2961 inA: 8 odds.ratio: 0.6936 pval: 0.88089 Jaccard: 0.0026033 is.tested: true
HGT.list notA: 25898 inA: 904 notA: 2860 inA: 109 odds.ratio: 1.0919 pval: 0.21114 Jaccard: 0.028144 is.tested: true
HGTNewNames.list notA: 26673 inA: 129 notA: 2951 inA: 18 odds.ratio: 1.2612 pval: 0.21235 Jaccard: 0.0058102 is.tested: true
HGTRevised.list notA: 26655 inA: 147 notA: 2965 inA: 4 odds.ratio: 0.24463 pval: 0.99988 Jaccard: 0.0012837 is.tested: true
KnownEffectorLTR.list notA: 26797 inA: 5 notA: 2969 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
KnownEffectorTIR.list notA: 26788 inA: 14 notA: 2966 inA: 3 odds.ratio: 1.9354 pval: 0.2369 Jaccard: 0.0010057 is.tested: true
KnownEffectorTandem.list notA: 26770 inA: 32 notA: 2963 inA: 6 odds.ratio: 1.694 pval: 0.17308 Jaccard: 0.0019993 is.tested: true
NonRedundantLtrRetroelementMerge.list notA: 25661 inA: 1141 notA: 2709 inA: 260 odds.ratio: 2.1584 pval: 1.0265e-23 Jaccard: 0.06326 is.tested: true
NotAllPredictedEffectorLTR.list notA: 25682 inA: 1120 notA: 2710 inA: 259 odds.ratio: 2.1916 pval: 2.1326e-24 Jaccard: 0.063341 is.tested: true
NotAllPredictedEffectorTIR.list notA: 25209 inA: 1593 notA: 2705 inA: 264 odds.ratio: 1.5444 pval: 1.2563e-09 Jaccard: 0.057869 is.tested: true
NotAllPredictedEffectorTandem.list notA: 21396 inA: 5406 notA: 2154 inA: 815 odds.ratio: 1.4975 pval: 1.5573e-19 Jaccard: 0.097313 is.tested: true
NotDorsalEffectorLTR.list notA: 25667 inA: 1135 notA: 2709 inA: 260 odds.ratio: 2.1703 pval: 5.4307e-24 Jaccard: 0.063353 is.tested: true
NotDorsalEffectorTIR.list notA: 25170 inA: 1632 notA: 2701 inA: 268 odds.ratio: 1.5303 pval: 2.0133e-09 Jaccard: 0.058248 is.tested: true
NotDorsalEffectorTandem.list notA: 21325 inA: 5477 notA: 2147 inA: 822 odds.ratio: 1.4907 pval: 2.963e-19 Jaccard: 0.097324 is.tested: true
NotKnownEffectorLTR.list notA: 25666 inA: 1136 notA: 2709 inA: 260 odds.ratio: 2.1684 pval: 6.0412e-24 Jaccard: 0.063337 is.tested: true
NotKnownEffectorTIR.list notA: 25172 inA: 1630 notA: 2701 inA: 268 odds.ratio: 1.5323 pval: 1.8169e-09 Jaccard: 0.058274 is.tested: true
NotKnownEffectorTandem.list notA: 21326 inA: 5476 notA: 2146 inA: 823 odds.ratio: 1.4935 pval: 1.9777e-19 Jaccard: 0.097454 is.tested: true
NotPredictedEffectorLTR.list notA: 25679 inA: 1123 notA: 2710 inA: 259 odds.ratio: 2.1854 pval: 2.9499e-24 Jaccard: 0.063294 is.tested: true
NotPredictedEffectorTIR.list notA: 25203 inA: 1599 notA: 2705 inA: 264 odds.ratio: 1.5383 pval: 1.7189e-09 Jaccard: 0.057793 is.tested: true
NotPredictedEffectorTandem.list notA: 21371 inA: 5431 notA: 2153 inA: 816 odds.ratio: 1.4914 pval: 3.3172e-19 Jaccard: 0.097143 is.tested: true
PredictedEffector.list notA: 26544 inA: 258 notA: 2935 inA: 34 odds.ratio: 1.1918 pval: 0.19305 Jaccard: 0.010536 is.tested: true
PredictedEffectorLTR.list notA: 26784 inA: 18 notA: 2968 inA: 1 odds.ratio: 0.50136 pval: 0.86422 Jaccard: 0.00033478 is.tested: true
PredictedEffectorTIR.list notA: 26757 inA: 45 notA: 2962 inA: 7 odds.ratio: 1.4052 pval: 0.25856 Jaccard: 0.0023225 is.tested: true
PredictedEffectorTandem.list notA: 26725 inA: 77 notA: 2956 inA: 13 odds.ratio: 1.5264 pval: 0.11055 Jaccard: 0.0042679 is.tested: true
RepeatAffectedGenesNoSimple.list notA: 16334 inA: 10468 notA: 1080 inA: 1889 odds.ratio: 2.7291 pval: 2.0423e-144 Jaccard: 0.14058 is.tested: true
SNPDensityAll0SNPS.list notA: 22190 inA: 4612 notA: 2969 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
SNPDensityAll10Percentile.list notA: 23832 inA: 2970 notA: 2969 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
SNPDensityAll10percAfterRemoveZeros.list notA: 24286 inA: 2516 notA: 2969 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
SNPDensityAll90Percentile.list notA: 26802 inA: 0 notA: 0 inA: 2969 odds.ratio: Infinity pval: 0 Jaccard: 1 is.tested: true
Secretome.gene.list notA: 24756 inA: 2046 notA: 2793 inA: 176 odds.ratio: 0.76247 pval: 0.99976 Jaccard: 0.035095 is.tested: true
SupportedIRFMergeClassified.list notA: 25158 inA: 1644 notA: 2698 inA: 271 odds.ratio: 1.5371 pval: 1.1741e-09 Jaccard: 0.058747 is.tested: true
tandem.gene.list notA: 21294 inA: 5508 notA: 2140 inA: 829 odds.ratio: 1.4976 pval: 9.439e-20 Jaccard: 0.097794 is.tested: true
ls -1 *list |awk '{print "go.obj <- newGeneOverlap("$1"$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)"}' |awk '{print $0"\ngo.obj"NR" <- testGeneOverlap(go.obj)"}' |less
####################################################
go.obj <- newGeneOverlap(x121EffectorOnlyNewGeneNames.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj1 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllGenes.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj2 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllHGTRevised.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj3 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj4 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj5 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj6 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(AllPredictedEffectors.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj7 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj8 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj9 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsalEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj10 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(DorsallikeGenesFixed.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj11 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family976.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj12 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Family1265.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj13 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGT.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj14 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTNewNames.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj15 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(HGTRevised.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj16 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj17 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj18 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(KnownEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj19 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NonRedundantLtrRetroelementMerge.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj20 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj21 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj22 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotAllPredictedEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj23 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj24 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj25 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotDorsalEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj26 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj27 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj28 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotKnownEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj29 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj30 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj31 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(NotPredictedEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj32 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffector.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj33 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorLTR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj34 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTIR.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj35 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(PredictedEffectorTandem.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj36 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(RepeatAffectedGenesNoSimple.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj37 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll0SNPS.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj38 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll10Percentile.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj39 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll10percAfterRemoveZeros.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj40 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SNPDensityAll90Percentile.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj41 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(Secretome.gene.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj42 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(SupportedIRFMergeClassified.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj43 <- testGeneOverlap(go.obj)
go.obj <- newGeneOverlap(tandem.gene.list$V1, SNPDensityAll0SNPS.list$V1, genome.size=All.genes)
go.obj44 <- testGeneOverlap(go.obj)
####################################################
#generate the commands to perform the analysis
AllCombine <- c(go.obj1, go.obj2, go.obj3, go.obj4, go.obj5, go.obj6, go.obj7, go.obj8, go.obj9, go.obj10, go.obj11, go.obj12, go.obj13, go.obj14, go.obj15, go.obj16, go.obj17, go.obj18, go.obj19, go.obj20, go.obj21, go.obj22, go.obj23, go.obj24, go.obj25, go.obj26, go.obj27, go.obj28, go.obj29, go.obj30, go.obj31, go.obj32, go.obj33, go.obj34, go.obj35, go.obj36, go.obj37, go.obj38, go.obj39, go.obj40, go.obj41, go.obj42, go.obj43, go.obj44)
library(RJSONIO)
exportJSON <- toJSON(AllCombine)
write(exportJSON,"SNPDensityAll0SNPS.list.out")
ls -1 *list |paste - <(less SNPDensityAll0SNPS.list.out|sed 's/\[/\t/g' |awk 'NF<15' |grep "\"" | sed '0~5 s/$/\nwait/g' |tr "\n" "\t" |sed 's/wait/\n/g' |sed 's/,/\t/g' |sed 's/"//g' |cut -f 1-7,9- |sed 's/}//g') |less -S
121EffectorOnlyNewGeneNames.list notA: 25052 inA: 107 notA: 4598 inA: 14 ] pval: 0.91097 Jaccard: 0.0029667 is.tested: true
AllGenes.list notA: 25158 inA: 1 notA: 4612 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
AllHGTRevised.list notA: 23861 inA: 1298 notA: 4352 inA: 260 odds.ratio: 1.0983 pval: 0.096817 Jaccard: 0.043993 is.tested: true
AllPredictedEffectorLTR.list notA: 25145 inA: 14 notA: 4604 inA: 8 odds.ratio: 3.1207 pval: 0.01373 Jaccard: 0.0017294 is.tested: true
AllPredictedEffectorTIR.list notA: 25112 inA: 47 notA: 4601 inA: 11 odds.ratio: 1.2774 pval: 0.28128 Jaccard: 0.002361 is.tested: true
AllPredictedEffectorTandem.list notA: 25070 inA: 89 notA: 4585 inA: 27 odds.ratio: 1.6587 pval: 0.017746 Jaccard: 0.0057435 is.tested: true
AllPredictedEffectors.list notA: 24806 inA: 353 notA: 4534 inA: 78 odds.ratio: 1.2089 pval: 0.077142 Jaccard: 0.01571 is.tested: true
DorsalEffectorLTR.list notA: 25153 inA: 6 notA: 4612 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
DorsalEffectorTIR.list notA: 25144 inA: 15 notA: 4612 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
DorsalEffectorTandem.list notA: 25123 inA: 36 notA: 4610 inA: 2 odds.ratio: 0.30277 pval: 0.98675 Jaccard: 0.00043029 is.tested: true
Dorsal-likeGenesFixed.list notA: 25007 inA: 152 notA: 4604 inA: 8 odds.ratio: 0.28588 pval: 0.99999 Jaccard: 0.0016793 is.tested: true
Family976.list notA: 25082 inA: 77 notA: 4588 inA: 24 odds.ratio: 1.7039 pval: 0.019185 Jaccard: 0.0051184 is.tested: true
Family1265.list notA: 25081 inA: 78 notA: 4578 inA: 34 odds.ratio: 2.3881 pval: 5.4716e-05 Jaccard: 0.0072495 is.tested: true
HGT.list notA: 24326 inA: 833 notA: 4432 inA: 180 odds.ratio: 1.186 pval: 0.02454 Jaccard: 0.033058 is.tested: true
HGTNewNames.list notA: 25035 inA: 124 notA: 4589 inA: 23 odds.ratio: 1.0119 pval: 0.51441 Jaccard: 0.0048564 is.tested: true
HGTRevised.list notA: 25034 inA: 125 notA: 4586 inA: 26 odds.ratio: 1.1354 pval: 0.31032 Jaccard: 0.0054887 is.tested: true
KnownEffectorLTR.list notA: 25156 inA: 3 notA: 4610 inA: 2 odds.ratio: 3.6377 pval: 0.1739 Jaccard: 0.00043337 is.tested: true
KnownEffectorTIR.list notA: 25144 inA: 15 notA: 4610 inA: 2 odds.ratio: 0.72724 pval: 0.76468 Jaccard: 0.00043225 is.tested: true
KnownEffectorTandem.list notA: 25129 inA: 30 notA: 4604 inA: 8 odds.ratio: 1.4555 pval: 0.22699 Jaccard: 0.0017234 is.tested: true
NonRedundantLtrRetroelementMerge.list notA: 24055 inA: 1104 notA: 4315 inA: 297 odds.ratio: 1.4997 pval: 3.8962e-09 Jaccard: 0.051959 is.tested: true
NotAllPredictedEffectorLTR.list notA: 24069 inA: 1090 notA: 4323 inA: 289 odds.ratio: 1.4762 pval: 2.0179e-08 Jaccard: 0.050684 is.tested: true
NotAllPredictedEffectorTIR.list notA: 23752 inA: 1407 notA: 4162 inA: 450 odds.ratio: 1.8251 pval: 2.4807e-24 Jaccard: 0.074763 is.tested: true
NotAllPredictedEffectorTandem.list notA: 20280 inA: 4879 notA: 3270 inA: 1342 odds.ratio: 1.7058 pval: 2.5775e-47 Jaccard: 0.1414 is.tested: true
NotDorsalEffectorLTR.list notA: 24061 inA: 1098 notA: 4315 inA: 297 odds.ratio: 1.5083 pval: 2.4763e-09 Jaccard: 0.052014 is.tested: true
NotDorsalEffectorTIR.list notA: 23720 inA: 1439 notA: 4151 inA: 461 odds.ratio: 1.8305 pval: 4.7813e-25 Jaccard: 0.076186 is.tested: true
NotDorsalEffectorTandem.list notA: 20227 inA: 4932 notA: 3245 inA: 1367 odds.ratio: 1.7276 pval: 5.509e-50 Jaccard: 0.14323 is.tested: true
NotKnownEffectorLTR.list notA: 24058 inA: 1101 notA: 4317 inA: 295 odds.ratio: 1.4932 pval: 6.1294e-09 Jaccard: 0.051637 is.tested: true
NotKnownEffectorTIR.list notA: 23720 inA: 1439 notA: 4153 inA: 459 odds.ratio: 1.8217 pval: 1.2733e-24 Jaccard: 0.075855 is.tested: true
NotKnownEffectorTandem.list notA: 20221 inA: 4938 notA: 3251 inA: 1361 odds.ratio: 1.7142 pval: 1.4478e-48 Jaccard: 0.14251 is.tested: true
NotPredictedEffectorLTR.list notA: 24066 inA: 1093 notA: 4323 inA: 289 odds.ratio: 1.4719 pval: 2.5008e-08 Jaccard: 0.050657 is.tested: true
NotPredictedEffectorTIR.list notA: 23746 inA: 1413 notA: 4162 inA: 450 odds.ratio: 1.8169 pval: 4.9852e-24 Jaccard: 0.074689 is.tested: true
NotPredictedEffectorTandem.list notA: 20255 inA: 4904 notA: 3269 inA: 1343 odds.ratio: 1.6968 pval: 1.7104e-46 Jaccard: 0.14113 is.tested: true
PredictedEffector.list notA: 24936 inA: 223 notA: 4543 inA: 69 odds.ratio: 1.6983 pval: 0.00016941 Jaccard: 0.014271 is.tested: true
PredictedEffectorLTR.list notA: 25148 inA: 11 notA: 4604 inA: 8 odds.ratio: 3.9723 pval: 0.004993 Jaccard: 0.0017305 is.tested: true
PredictedEffectorTIR.list notA: 25118 inA: 41 notA: 4601 inA: 11 odds.ratio: 1.4647 pval: 0.17231 Jaccard: 0.0023641 is.tested: true
PredictedEffectorTandem.list notA: 25095 inA: 64 notA: 4586 inA: 26 odds.ratio: 2.223 pval: 0.00090271 Jaccard: 0.0055603 is.tested: true
RepeatAffectedGenesNoSimple.list notA: 14920 inA: 10239 notA: 2494 inA: 2118 odds.ratio: 1.2375 pval: 2.3104e-11 Jaccard: 0.14262 is.tested: true
SNPDensityAll0SNPS.list notA: 25159 inA: 0 notA: 0 inA: 4612 odds.ratio: Infinity pval: 0 Jaccard: 1 is.tested: true
SNPDensityAll10Percentile.list notA: 25159 inA: 0 notA: 1642 inA: 2970 odds.ratio: Infinity pval: 0 Jaccard: 0.64397 is.tested: true
SNPDensityAll10percAfterRemoveZeros.list notA: 22643 inA: 2516 notA: 4612 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
SNPDensityAll90Percentile.list notA: 22190 inA: 2969 notA: 4612 inA: 0 odds.ratio: 0 pval: 1 Jaccard: 0 is.tested: true
Secretome.gene.list notA: 23166 inA: 1993 notA: 4383 inA: 229 odds.ratio: 0.60732 pval: 1 Jaccard: 0.034671 is.tested: true
SupportedIRFMergeClassified.list notA: 23705 inA: 1454 notA: 4151 inA: 461 odds.ratio: 1.8105 pval: 2.7293e-24 Jaccard: 0.075997 is.tested: true
tandem.gene.list notA: 20191 inA: 4968 notA: 3243 inA: 1369 odds.ratio: 1.7156 pval: 6.9682e-49 Jaccard: 0.1429 is.tested: true
ggplot(data=test, aes(y=V2,x =V1))+geom_violin(size=2,fill = "#FF6666") +labs(title="Gene Expression of Genomic Strata",y="log(Fold Change)",x="") +coord_flip(ylim=c(-10,11)) + xlim( "Genes with Repeat-overlapping Exons", "All Predicted Effectors in DNA Transposons", "DOG-box Genes in DNA Transposons", "Predicted Effectors in DNA Transposons", "Known Effectors in DNA Transposons", "Genes in DNA Transposons", "All Predicted Effectors in LTR Retroelements", "DOG-box Genes in LTR Retroelements", "Predicted Effectors in LTR Retroelements", "Known Effectors in LTR Retroelements", "Genes in LTR Retroelements", "All Predicted Effectors in TDR", "DOG-box Genes in TDR", "Predicted Effectors in TDR", "Known Effectors in TDR", "Genes in TDR", "High Confidence HGT", "All Predicted Effectors", "DOG-box Genes", "Predicted Effectors", "Known Effectors", "All Genes") + scale_colour_manual(values = cols) + theme(plot.title = element_text(hjust = 0.5),axis.text = element_text(size = 46),title = element_text(size = 60),axis.ticks = element_line(colour = "black", size = 3),text = element_text( size = 30))
ggplot(data=SNPDensity4BoxPlot, aes(y=V2,x =V1))+geom_violin(size=2,fill = "#FF6666") +labs(title="SNP Density of Genomic Strata",y="log(SNP/CDS Length)",x="") +coord_flip(ylim=c(-10,0)) + xlim("Genes with Repeat-overlapping Exons", "All Predicted Effectors in DNA Transposons", "DOG-box Genes in DNA Transposons", "Predicted Effectors in DNA Transposons", "Known Effectors in DNA Transposons", "Genes in DNA Transposons","All Predicted Effectors in LTR Retroelements", "DOG-box Genes in LTR Retroelements", "Predicted Effectors in LTR Retroelements", "Known Effectors in LTR Retroelements", "Genes in LTR Retroelements", "All Predicted Effectors in TDR", "DOG-box Genes in TDR", "Predicted Effectors in TDR", "Known Effectors in TDR", "Genes in TDR", "High Confidence HGT", "All Predicted Effectors", "DOG-box Genes", "Predicted Effectors", "Known Effectors", "All Genes") + scale_colour_manual(values = cols) + theme(plot.title = element_text(hjust = 0.5),axis.text = element_text(size = 46),title = element_text(size = 60),axis.ticks = element_line(colour = "black", size = 3),text = element_text( size = 30))