R/get_tabcalls_path.R

In abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

get_tabcalls_path <- function(TableSif,outdir,outdir.calls.name){
  tabsnvs_index <- TableSif[,c(1,2,4)]
  tabsnvs_index$tabcalls_f1 <- NA
  tabsnvs_index$tabcalls_f2 <- NA
  tabsnvs_index$tabcalls_f3 <- NA
  for(i in 1:nrow(TableSif)){
    xcs <- list.files(file.path(outdir,outdir.calls.name,tabsnvs_index$plasma[i]),recursive = FALSE,full.names = TRUE,pattern = "pmtab_")
    tabsnvs_index$tabcalls_f1[i] <- grep(xcs, pattern = "pmtab_F1", value = TRUE)
    tabsnvs_index$tabcalls_f2[i] <- grep(xcs, pattern = "pmtab_F2", value = TRUE)
    tabsnvs_index$tabcalls_f3[i] <- grep(xcs, pattern = "pmtab_F3", value = TRUE)
  }
  return( tabsnvs_index )
}