R/read_varscan_data.R

In ucl-pathgenomics/cmvdrg: Human CMV Drug Resistance Genotyping

#' Handles varscan data
#'
#' reads varscan files & returns a formatted data.frame
#'
#' @param f.df data.frame of read varscan file
#' @return formatted data.frame
#' @keywords internal
#' @export
#' 

read_varscan_data <- function(f.df){
  #reads a single file of varscan data
  
  #dat <- read.table(file = inFile$datapath, header = T, as.is = T, sep = "\t")
  #dat <- read.table(file = inFile, header = T, as.is = T, sep = "\t")
  dat <- f.df
  dat$id = "single run"
  df.het <- as.data.frame(matrix(unlist(strsplit(dat[,5], split=":")), ncol=6, byrow="T"), stringsAsFactors=F)
  all <- cbind(dat[,1:4], df.het[,1:5], dat[,6],dat[,12]) # shifted from in-house 
  colnames(all)[5]<-"Var_touse"
  colnames(all)[6]<-"something"
  colnames(all)[7]<-"Ref.count"
  colnames(all)[8]<-"Var.count"
  colnames(all)[9]<-"VarFreq"
  colnames(all)[10]<-"StrandFilter"
  colnames(all)[11]<-"Sample"
  all$Var_touse <- NULL
  all$StrandFilter <- NULL
  all$something <- NULL
  all$Chrom <- NULL
  return(all)
}