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NoiSeq commands in R for samples without replicates
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NoiSeq commands in R for samples without replicates
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library(GenomicFeatures)
library("Rsamtools")
library( "GenomicAlignments" )
library("NOISeq")
library("biomaRt")
library("tidyverse")
head(assay(se))
colSums(assay(se))
rowData(se)
head(colnames(se))
countData<-assay(se)
head(countData)
mydata <- assay(se)
write.table(mydata, "coldata_6hr.txt", sep = "\t")
colData_6hr <- read.table("coldata1_6hr.txt", sep = '\t', header = TRUE)
head(colData_6hr)
sink('6hrnoiseq.doc', append=TRUE)
myfactors <- data.frame(group = c("Control", "Treatment"))
myData <- readData(data=colData_6hr, factor=myfactors)
myresults <- noiseq(myData, factor = "group", k = 0, norm = "n", pnr = 0.2, nss = 5, v = 0.02, lc = 1, replicates = "no")
myresults
save(myresults, file = "sixhrResults.RData")
myresults@method
myresults@k
myresults@lc
myresults@factor
myresults@comparison
head(myresults@results[[1]])
myresults.deg = degenes(myresults, q = 0.8, M = NULL)
head(myresults.deg[[1]])
DE.plot(myresults, q = 0.8, graphic = "expr", log.scale = TRUE)
write.csv(myresults.deg, file="DEGs_myresults.csv")
#Can use any of the two types of normalization (RPKM & UQUA) depending on the data
myRPKM = rpkm(assayData(myData)$exprs, k = 0, lc = 1)
head(myRPKM)
mynoiseqrpkm <- noiseq(myData, factor = "group", k = 0.5, norm = "rpkm", pnr = 0.2, nss = 5, v = 0.02, lc = 1, replicates = "no")
mynoiseqrpkm
save(mynoiseqrpkm, file = "sixhrrpkm.RData")
head(mynoiseqrpkm@results[[1]])
head(mynoiseqrpkm@results)
mynoiseqrpkm.deg = degenes(mynoiseqrpkm, q = 0.8, M = NULL)
head(mynoiseqrpkm.deg[[1]])
DE.plot(mynoiseqrpkm, q = 0.8, graphic = "expr", log.scale = TRUE)
write.csv(mynoiseqrpkm.deg, file="DEGs_mynoiseqrpkm.csv")
mynoiseqrpkm1.deg = degenes(mynoiseqrpkm, q = 0.5, M = NULL)
head(mynoiseqrpkm1.deg[[1]])
DE.plot(mynoiseqrpkm, q = 0.5, graphic = "expr", log.scale = TRUE)
write.csv(mynoiseqrpkm1.deg, file="DEGs_mynoiseqrpkm1.csv")
myUQUA = uqua(assayData(myData)$exprs, lc = 0.5, k = 0)
head(myUQUA)
mynoiseququa <- noiseq(myData, factor = "group", k = 0.5, norm = "uqua", pnr = 0.2, nss = 5, v = 0.02, lc = 1, replicates = "no")
mynoiseququa
save(mynoiseququa, file = "sixhruqua.RData")
head(mynoiseququa@results[[1]])
head(mynoiseququa@results)
mynoiseququa.deg = degenes(mynoiseququa, q = 0.8, M = NULL)
head(mynoiseququa.deg[[1]])
DE.plot(mynoiseququa, q = 0.8, graphic = "expr", log.scale = TRUE)
write.csv(mynoiseququa.deg, file="DEGs_mynoiseququa.csv")
mynoiseququa1.deg = degenes(mynoiseququa, q = 0.5, M = NULL)
head(mynoiseququa1.deg[[1]])
DE.plot(mynoiseququa, q = 0.5, graphic = "expr", log.scale = TRUE)
write.csv(mynoiseququa1.deg, file="DEGs_mynoiseququa1.csv")