Commit 2d36059b authored by Kosmas Hench's avatar Kosmas Hench
Browse files

include 2.2.9 selscan scripts

parent a4fd034b

0_data/0_resources/iHH.config

0 → 100644
+12 −0
Original line number Original line Diff line number Diff line 
nig

pue

uni

nigbel

puebel

unibel

nighon

puehon

unihon

nigboc

pueboc

uniboc
 
 No newline at end of file

0_data/0_scripts/S11.getIHH12.R

0 → 100644
+37 −0
Original line number Original line Diff line number Diff line 
getIHH12 <- function(searchLG,xr){

  np <- read.csv(paste('./iHH12/',searchLG,'/iHH12.nig.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='nig')

  nu <- read.csv(paste('./iHH12/',searchLG,'/iHH12.pue.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='pue')

  pu <- read.csv(paste('./iHH12/',searchLG,'/iHH12.uni.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='uni')

  

  data_iHH12 <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(iHH[12])')

  

  npB <- read.csv(paste('./iHH12/',searchLG,'/iHH12.nigbel.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='nig',group='bel')

  nuB <- read.csv(paste('./iHH12/',searchLG,'/iHH12.puebel.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='pue',group='bel')

  puB <- read.csv(paste('./iHH12/',searchLG,'/iHH12.unibel.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='uni',group='bel')

  

  npH <- read.csv(paste('./iHH12/',searchLG,'/iHH12.puehon.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='nig',group='hon')

  nuH <- read.csv(paste('./iHH12/',searchLG,'/iHH12.puehon.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='pue',group='hon')

  puH <- read.csv(paste('./iHH12/',searchLG,'/iHH12.unihon.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='uni',group='hon')

  

  npP <- read.csv(paste('./iHH12/',searchLG,'/iHH12.nigboc.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='nig',group='pan') 

  nuP <- read.csv(paste('./iHH12/',searchLG,'/iHH12.pueboc.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='pue',group='pan')

  puP <- read.csv(paste('./iHH12/',searchLG,'/iHH12.uniboc.selscan-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGihh12) %>% mutate(run='uni',group='pan')

  

  data_iHH12_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(ind~iHH[12])')

  

  

  return(list(data_iHH12_pw=data_iHH12_pw,data_iHH12=data_iHH12))

}
 
 No newline at end of file

0_data/0_scripts/S11.getPI.R

0 → 100644
+37 −0
Original line number Original line Diff line number Diff line 
getPI<- function(searchLG,xr){

  np <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.nig.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig')

  nu <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.pue.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue')

  pu <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.uni.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='uni')

  

  data_pi <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(pi)')

  

  npB <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.nigbel.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig',group='bel')

  nuB <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.puebel.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue',group='bel')

  puB <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.unibel.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='uni',group='bel')

  

  npH <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.nighon.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig',group='hon')

  nuH <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.puehon.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue',group='hon')

  puH <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.unihon.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='uni',group='hon')

  

  npP <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.nigboc.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig',group='pan') 

  nuP <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.pueboc.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue',group='pan')

  puP <- read.csv(gzfile(paste('./pi/',searchLG,'/dxy.uniboc.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='uni',group='pan')

  

  data_pi_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(ind~pi)')

  

  

  return(list(data_pi_pw=data_pi_pw,data_pi=data_pi))

}
 
 No newline at end of file

0_data/0_scripts/S11.getPIpw.R

0 → 100644
+37 −0
Original line number Original line Diff line number Diff line 
getPIpw<- function(searchLG,xr){

  np <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.pue-nig.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-pue')

  nu <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.nig-uni.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-uni')

  pu <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.uni-pue.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue-uni')

  

  data_pi <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(pi~pw)')

  

  npB <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.puebel-nigbel.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-pue',group='bel')

  nuB <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.nigbel-unibel.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-uni',group='bel')

  puB <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.unibel-puebel.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue-uni',group='bel')

  

  npH <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.puehon-nighon.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-pue',group='hon')

  nuH <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.nighon-unihon.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-uni',group='hon')

  puH <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.unihon-puehon.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue-uni',group='hon')

  

  npP <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.pueboc-nigboc.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-pue',group='pan') 

  nuP <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.nigboc-uniboc.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='nig-uni',group='pan')

  puP <- read.csv(gzfile(paste('./pi_pw/',searchLG,'/dxy.uniboc-pueboc.',searchLG,'-10kb-1kb.windowed.pi.gz',sep='')),sep='\t') %>% 

    select(BIN_START,BIN_END,PI) %>% mutate(run='pue-uni',group='pan')

  

  data_pi_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(pw~pi~pw)')

  

  

  return(list(data_piPW_pw=data_pi_pw,data_piPW=data_pi))

}
 
 No newline at end of file

0_data/0_scripts/S11.getXPEHH.R

0 → 100644
+37 −0
Original line number Original line Diff line number Diff line 
getXPEHH <- function(searchLG,xr){

  np <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.pue-nig-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-pue')

  nu <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.nig-uni-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-uni')

  pu <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.pue-uni-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='pue-uni')

  

  data_xpEHH <- rbind(np,nu,pu) %>% mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(xpEHH)')

  

  npB <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.puebel-nigbel-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-pue',group='bel')

  nuB <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.nigbel-unibel-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-uni',group='bel')

  puB <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.puebel-unibel-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='pue-uni',group='bel')

  

  npH <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.puehon-nighon-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-pue',group='hon')

  nuH <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.nighon-unihon-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-uni',group='hon')

  puH <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.puehon-unihon-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='pue-uni',group='hon')

  

  npP <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.pueboc-nigboc-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-pue',group='pan') 

  nuP <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.nigboc-uniboc-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='nig-uni',group='pan')

  puP <- read.csv(paste('./xpEHH/',searchLG,'/xpEHH.pueboc-uniboc-',searchLG,'-10kb-1kb.txt',sep=''),sep='\t') %>% 

    select(BIN_START,BIN_END,AVGxxEHH) %>% mutate(run='pue-uni',group='pan')

  

  data_xpEHH_pw <- rbind(npB,nuB,puB,npH,nuH,puH,npP,nuP,puP) %>%

    mutate(POS=(BIN_START+BIN_END)/2,window='bolditalic(pw~xpEHH)')

  

  

  return(list(data_xpEHH_pw=data_xpEHH_pw,data_xpEHH=data_xpEHH))

}
 
 No newline at end of file