#' RFMix
#'
#' \code{create_input_RFMix}
#'
#' @param H1 a haplotype matrix.
#' @param H2 a haplotype matrix.
#' @param Hadm a haplotype matrix.
#' @param genetic.map a numerical vector.
#' @param RFMix.output a character string.
#'
#' @return
#'
#' @export
#'
create_input_RFMix = function(H1,
H2,
Hadm,
genetic.map,
RFMix.output = "RFMix"){
G <- cbind(H1, H2, Hadm)
write.table(t(G),
paste0(RFMix.output, "_alleles.lfmm"),
col.names = FALSE,
row.names = FALSE,
quote = FALSE)
LEA::lfmm2geno(paste0(RFMix.output, "_alleles.lfmm"),
paste0(RFMix.output, "_alleles.geno"),
force = TRUE)
file.remove(paste0(RFMix.output, "_alleles.lfmm"))
file.rename(paste0(RFMix.output, "_alleles.geno"),
paste0(RFMix.output, "_alleles.txt"))
formatted.genetic.map <- format(genetic.map,
scientific = FALSE,
nsmall = 8)
write.table(formatted.genetic.map,
paste0(RFMix.output, "_markerLocation.txt"),
sep = "\n",
col.names = FALSE,
row.names = FALSE,
quote = FALSE)
pop <- c(rep(1, ncol(H1)), rep(2, ncol(H2)), rep(0, ncol(Hadm)))
l3 <- stringr::str_c(pop, collapse = " ")
con <- file(paste0(RFMix.output, "_classes.txt"))
writeLines(l3, con = con)
close(con = con)
}
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