R/codif.data.R

In BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

#######################################################################
#                                                                     #
# Package: BatchMap                                                     #
#                                                                     #
# File: codif.data.R                                                  #
# Contains: codif.data                                                #
#                                                                     #
# Written by Marcelo Mollinari                                        #
# copyright (c) 2009, Marcelo Mollinari                               #
#                                                                     #
# On Decemter 12th, 2015, Gabriel Margarido included codification     #
# for other cross types.                                              #
#                                                                     #
# First version: 02/27/2009                                           #
# Last update: 12/12/2015                                             #
# License: GNU General Public License version 2 (June, 1991) or later #
#                                                                     #
#######################################################################

# This function gets the input in strings and converts into numbers
codif.data <- function(geno.in, segr.type.in,
                       cross = c("outcross")) {
  cross <- match.arg(cross)

  geno.out <- matrix(NA,nrow(geno.in),ncol(geno.in))
  segr.type.out <- rep(NA,length(segr.type.in))

  ## missing data are represented by '0'
  geno.out[is.na(geno.in)] <- 0

  for(i in 1:length(segr.type.in)) {
    ## based on the marker type, convert strings to numbers
    switch(EXPR=segr.type.in[i],
           A.1={
             geno.out[which(geno.in[,i]=="ac"),i] <- 1
             geno.out[which(geno.in[,i]=="ad"),i] <- 2
             geno.out[which(geno.in[,i]=="bc"),i] <- 3
             geno.out[which(geno.in[,i]=="bd"),i] <- 4
             segr.type.out[i] <- 1
           },
           A.2={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="ac"),i] <- 2
             geno.out[which(geno.in[,i]=="ba"),i] <- 3
             geno.out[which(geno.in[,i]=="bc"),i] <- 4
             segr.type.out[i] <- 1
           },
           A.3={
             geno.out[which(geno.in[,i]=="ac"),i] <- 1
             geno.out[which(geno.in[,i]=="a"),i] <- 2
             geno.out[which(geno.in[,i]=="bc"),i] <- 3
             geno.out[which(geno.in[,i]=="b"),i] <- 4
             segr.type.out[i] <- 1
           },
           A.4={
             geno.out[which(geno.in[,i]=="ab"),i] <- 1
             geno.out[which(geno.in[,i]=="a"),i] <- 2
             geno.out[which(geno.in[,i]=="b"),i] <- 3
             geno.out[which(geno.in[,i]=="o"),i] <- 4
             segr.type.out[i] <- 1
           },
           B1.5={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="ab"),i] <- 2
             geno.out[which(geno.in[,i]=="b"),i] <- 3
             segr.type.out[i] <- 2
           },
           B2.6={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="ab"),i] <- 2
             geno.out[which(geno.in[,i]=="b"),i] <- 3
             segr.type.out[i] <- 3
           },
           B3.7={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="ab"),i] <- 2
             geno.out[which(geno.in[,i]=="b"),i] <- 3
             segr.type.out[i] <- 4
           },
           C.8={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="o"),i] <- 2
             segr.type.out[i] <- 5
           },
           D1.9={
             geno.out[which(geno.in[,i]=="ac"),i] <- 1
             geno.out[which(geno.in[,i]=="bc"),i] <- 2
             segr.type.out[i] <- 6
           },
           D1.10={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="ab"),i] <- 2
             segr.type.out[i] <- 6
           },
           D1.11={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="b"),i] <- 2
             segr.type.out[i] <- 6
           },
           D1.12={
             geno.out[which(geno.in[,i]=="ab"),i] <- 1
             geno.out[which(geno.in[,i]=="a"),i] <- 2
             segr.type.out[i] <- 6
           },
           D1.13={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="o"),i] <- 2
             segr.type.out[i] <- 6
           },
           D2.14={
             geno.out[which(geno.in[,i]=="ac"),i] <- 1
             geno.out[which(geno.in[,i]=="bc"),i] <- 2
             segr.type.out[i] <- 7
           },
           D2.15={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="ab"),i] <- 2
             segr.type.out[i] <- 7
           },
           D2.16={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="b"),i] <- 2
             segr.type.out[i] <- 7
           },
           D2.17={
             geno.out[which(geno.in[,i]=="ab"),i] <- 1
             geno.out[which(geno.in[,i]=="a"),i] <- 2
             segr.type.out[i] <- 7
           },
           D2.18={
             geno.out[which(geno.in[,i]=="a"),i] <- 1
             geno.out[which(geno.in[,i]=="o"),i] <- 2
             segr.type.out[i] <- 7
           }
    )
    if(any(is.na(geno.out[,i])))
      stop(paste("Invalid marker codification. Please check data for marker",
                 colnames(geno.in)[i]), ".", sep="")
  }
  dimnames(geno.out) <- dimnames(geno.in)
  return(list(geno.out, segr.type.out))
}

# end of file