R/solGS/combine_gebvs_files.r

   1 #combines gebvs of traits of a population
   2 # Isaak Y Tecle
   3
   4
   5 options(echo = FALSE)
   6
   7
   8 allArgs <- commandArgs()
   9
  10 inFile <- grep("gebv_files",
  11                allArgs,
  12                ignore.case = TRUE,
  13                perl = TRUE,
  14                value = TRUE
  15                )
  16
  17 outputFile <- grep("combined_gebvs",
  18                 allArgs,
  19                 ignore.case = TRUE,
  20                 perl = TRUE,
  21                 value = TRUE
  22                 )
  23
  24 inputFiles <- scan(inFile,
  25                    what = "character"
  26                    )
  27
  28
  29 combinedGebvs <- c()
  30 count         <- 0
  31
  32 for (i in inputFiles) {
  33
  34   traitGebv <- read.table(i,
  35                           header = TRUE,
  36                           row.names = NULL,
  37                           sep = "\t",
  38                           dec = "."
  39                           )
  40
  41   trait <- colnames(traitGebv)
  42   count <- count + 1
  43
  44   traitGebv <- traitGebv[order(traitGebv$X), ]
  45
  46   if(count == 1) {
  47     combinedGebvs <- traitGebv
  48
  49     row.names(combinedGebvs) <- combinedGebvs[, 1]
  50     combinedGebvs[, 1] <- NULL
  51
  52   } else {
  53     row.names(traitGebv) <- traitGebv[, 1]
  54     traitGebv[, 1] <- NULL
  55
  56     combinedGebvs <- merge(traitGebv,
  57                            combinedGebvs,
  58                            by=0,
  59                            all=FALSE
  60                            )
  61
  62     rownames(combinedGebvs) <- combinedGebvs[, 1]
  63     combinedGebvs$Row.names <- NULL
  64   }
  65 }
  66
  67 if (length(outputFile) != 0 ) {
  68   write.table(combinedGebvs,
  69               file = outputFile,
  70               sep = "\t",
  71               quote = FALSE,
  72               col.names = NA,
  73               )
  74 }
  75
  76 q(save = "no", runLast = FALSE)