R/index.genotype.R

In dgarrimar/sQTLseekeR2: R package for splicing QTL mapping

##' Index genotype file. The file must be tab-separated and ordered by chr, start, end
##' position. Moreover, the first four columns must contain 'chr', 'start', 'end' and 'snpId'
##' information. Then each additional column is named using a sample ID and represents
##' its genotype. The genotype is coded as follow: 0 for ref/ref, 1 for ref/mut, 2 for
##' mut/mut and -1 for missing values. The input file should be a text file.
##' @title Index the genotype file
##' @param file the name of the genotype file.
##' @return the name of the indexed genotype file.
##' @author Jean Monlong
##' @export
index.genotype <- function(file)
{
    if(!file.exists(file)){
        stop("File not found: ", file)
    }
    ## Check column names and order
    snp50 = utils::read.table(file, sep="\t", header=TRUE, quote = "", 
                              comment.char = "", as.is = TRUE, nrows = 50)
    if(!all(colnames(snp50)[1:4] == c("chr","start","end","snpId"))){
        stop("Missing column or in incorrect order. The first 4 columns must be 'chr', 'start', 'end' and 'snpId'.")
    }
    ## Check that genotypes are discrete
    if(length(unique(unlist(snp50[, -(1:4)]))) > 10){
        stop("Discrete genotypes are required but the inputed genotypes look continuous.")
    }
    file.final <- Rsamtools::bgzip(file, 
                                   dest = paste0(sub(".gz", "", file), ".bgz"), 
                                   overwrite = TRUE)
    Rsamtools::indexTabix(file.final, format = "bed")
    return(file.final)
}