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#' Read haplotype data, selected by region of interest, from PED files
#' (regular PLINK untransposed text files)
#'
#' @param filename character, path to PED file containing haplotype
#' data. Attention! filename should contain path to \code{<file>.ped}
#' with full file name. For example \code{../mydata/inputplink.ped}
#' @inheritParams read.haplo
#' @return matrix object containing the haplotypes selected by the
#' region of interest
#' @seealso \code{\link{read.haplo}},
#' \code{\link{read.haplo.bedfile}},
#' \code{\link{read.haplo.shapeit_haps}},
#' \code{\link{readMapFile}}
#' @import snpStats
#' @keywords internal
read.haplo.pedfile <- function(filename = "NULL",
map,
chr = "NULL",
startpos = "NULL",
endpos = "NULL"){
# TODO: probably we want to automatically append ".ped" to filename
# TODO: add extensions
snps2out <- map[which(map[, 1] == chr &
map[, 3] > startpos &
map[, 3] < endpos),
2]
plink.input <- snpStats::read.pedfile(file = filename,
snps = snps2out)
GenotypeMatrix <- methods::as(plink.input$genotypes, "numeric")
# TODO: added 'rownames(GenotypeMatrix) <- idNames' may required
return(GenotypeMatrix)
}
# tmp = read.haplo.pedfile(filename = "data.ped",map = tmp1,chr = 1,
# startpos = 9000, endpos = 25000)
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