R/read_snp_genotypes.R

In maialab/daeqtlr: DAEQTL Mapping

#' Import SNP genotypes
#'
#' This function reads in SNP genotypes from a text file. The data is expected
#' to be in tabular format. First column is expected to be the locus identity
#' (e.g. SNP identifier), and remaining columns are the samples. First column is
#' expected to be the locus identity (e.g. SNP identifier), and remaining
#' columns are the samples. The genotypes are expected to be encoded as `"AA"`,
#' `"AB"`, `"BA"` or `"BB"`.
#'
#' @param file A path to file.
#' @param sep The separator between columns.
#' @param header Does the first data line contain column names?
#' @param ... Extra arguments to be passed on to [data.table::fread()].
#'
#' @return A data frame of genotype values (`"AA"`, `"AB"`, `"BA"` or `"BB"`).
#'   Each row is for a locus. The locus identity is indicated in the first
#'   column and named \code{snp}. Remaining columns are samples.
#'
#' @md
#' @export
read_snp_genotypes <- function(file, sep = ',', header = TRUE, ...) {

  genotypes <- data.table::fread(input = file, sep = sep, header = header, ...)
  data.table::setnames(genotypes, 1L, "snp")
  data.table::setkeyv(genotypes, 'snp')

  # First column is the SNP identifier, remaining columns are samples.
  cols <- colnames(genotypes)[-1]

  # Convert genotype strings to factors
  for (j in cols)
    data.table::set(genotypes,
                    j = j,
                    value = factor(genotypes[[j]], levels = c('AA', 'AB', 'BA', 'BB')))

  genotypes
}