-
Notifications
You must be signed in to change notification settings - Fork 1
/
assignPOP_onePopLOOP_v1.R
37 lines (33 loc) · 1.55 KB
/
assignPOP_onePopLOOP_v1.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
################ establish refpops
library(assignPOP)
library(klaR)
library(mime)
library(genepopedit)
work_dir <- "/Users/macbook2017/Desktop/dapc/"
setwd(work_dir)
all.gen = "ec.287.2.500.6347.remove.outliers.gen.txt"
all.renamed.gen="all.renamed.gen"
species = "ec"
genepop_ID(genepop=all.gen, path=paste0(work_dir, all.renamed.gen))
PopNames.all <- genepop_detective(all.renamed.gen, variable="Pops")
PopCounts.all <- genepop_detective(all.renamed.gen, variable="PopNum")
PopCounts.all
for (i in PopNames.all) {
pop.sublist <- c("SCLS", i)
pop.sublistname <- paste(pop.sublist, collapse ="_", sep=".")
subset_genepop(genepop= all.renamed.gen, keep = TRUE,
spop = pop.sublist,
path = paste0(work_dir, paste(pop.sublistname, ".gen", sep="")))
used.PopNames <- genepop_detective(paste(pop.sublistname, ".gen", sep=""), variable="Pops")
all_ref <- read.Genepop(paste(pop.sublistname, ".gen", sep=""), pop.names=used.PopNames)
#all_inc <- read.Genepop( "nokin_allq9_inc.txt")
#all_ref_rd <- reduce.allele(all_ref, p = 0.95)
assign_trial = assign.MC(all_ref, train.inds=c(0.92), train.loci=c(0.8),
loci.sample="fst", iterations=200, dir = paste(species, pop.sublistname, "mc_svm/", sep="."), model="svm" )
accuMC <- accuracy.MC(dir = paste(species, pop.sublistname, "mc_svm/", sep="."))
pdf(file=paste(species, pop.sublistname, "assignpop.mc.plot.pdf", sep="."))
plot.result <- accuracy.plot(accuMC, pop = c("all", used.PopNames))
print(plot.result)
dev.off()
}
file.remove("all.renamed.gen")