data-raw/define_candidate_sets.R

In joshuamschmidt/multiPermr: What the Package Does in One 'Title Case' Line

# defining candidates for multistat
load("/Users/joshuaschmidt/Box/ancestral_chimp/allchr_pbs4_bahtia_nj_keep.neg.Rdata")
pbs_background <- allPBSNJ[,.(chr,start,end)]
setkey(pbs_background,chr,start,end)

allPBSNJ[,e.p:= (1-rank(e.s)/.N)]
allPBSNJ[,c.p:= (1-rank(c.s)/.N)]

eastern_candidates <- allPBSNJ[e.p < 0.0002472][,.(chr,start,end)]
setkey(eastern_candidates,chr,start,end)

central_candidates <- allPBSNJ[c.p < 0.00021][,.(chr,start,end)]
setkey(central_candidates,chr,start,end)

pclr <- fread("sed -e /Chr/d  /Users/joshuaschmidt/Box/ancestral_chimp/all.windows.3pclr.ce.nc.txt",
              select = c("V1","V2","V9"),
              col.names = c("chr","focal","LL"))
pclr[,focal:=as.integer(focal)]
setkey(pclr,chr,focal)
pclr[,p:= 1-(rank(LL)/.N)]
internal_candidates_focal <- pclr[p < 0.0054][,.(chr,start=focal,end=focal)]
internal_candidates_5kb <- pclr[p < 0.0054][,.(chr,start=focal-2500,end=focal+2500)]
setkey(internal_candidates_focal,chr,start,end)
setkey(internal_candidates_5kb,chr,start,end)

internal_background_focal <- pclr[,.(chr,start=focal,end=focal)]
internal_background_5kb <- pclr[,.(chr,start=focal-2500,end=focal+2500)]
setkey(internal_background_focal,chr,start,end)
setkey(internal_background_5kb,chr,start,end)


# defining candidates for single stat internal
internal_candidates_0.5 <- pclr[p < 0.005][,.(chr,start=focal,end=focal)]
internal_candidates_0.1 <- pclr[p < 0.001][,.(chr,start=focal,end=focal)]
internal_candidates_0.05 <- pclr[p < 0.0005][,.(chr,start=focal,end=focal)]
setkey(internal_candidates_0.5,chr,start,end)
setkey(internal_candidates_0.1,chr,start,end)
setkey(internal_candidates_0.05,chr,start,end)