# Lindsay V. Clark, 11 March 2013
# R function to import data from TASSEL's HapMap format to adegenet's
# genind format.
# Example use:
# mydata <- hapMap2genind("HapMap.hmp.txt")
hapMap2genind <- function(file){
    require(adegenet)
    hapmap <- read.table(file, header=TRUE, row.names=1, sep="\t",
                     stringsAsFactors=FALSE)
    samples <- names(hapmap)[11:length(hapmap)]
    conv <- c("AA", "CC", "TT", "GG", "AC", "AT", "AG", "CT", "CG", "TG", NA)
    names(conv) <- c("A", "C", "T", "G", "M" , "W", "R", "Y", "S",  "K", "N")
    mydf <- matrix(NA, nrow=dim(hapmap)[1], ncol=length(samples),
                   dimnames=list(row.names(hapmap), samples))
    for(i in 1:length(samples)){
        mydf[,i] <- conv[hapmap[[i+10]]]
    }
    mydf <- as.data.frame(t(mydf))
    x <- df2genind(mydf, type="codom")
    return(x)
}