#!/usr/bin/env Rscript
#---------------
# base libraries
#---------------
suppressMessages(pacman::p_load(dplyr,readr,tidyr,magrittr,purrr,stringr,rlist,ggplot2,crayon))
#-----------------
# path contingency
#-----------------
wd <- getwd()
if(!"samples.txt" %in% list.files()){
setwd("..")
}
#----------------
# read cncf files
#----------------
samples %>%
mutate(cncf=str_c("facets/",tumor,"_",normal,".cncf.txt")) %$%
cncf %>%
map(~
read.delim(.x,sep="\t",stringsAsFactors=FALSE) %>%
tbl_df %>%
select(tcn.em,lcn.em) %>%
mutate(loh=ifelse(tcn.em==0,TRUE,))
)
#--------------------------------
# move back to original directory
#--------------------------------
setwd(wd)
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