R/scan1_pattern.R

In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

#' @importFrom rlang .data
#' @importFrom dplyr filter mutate
#' 
pull_patterns <- function(patterns, pheno_names) {
  if(all(pheno_names %in% patterns$pheno)) {
    dplyr::filter(patterns, .data$pheno %in% pheno_names)
  }
  else {
    out <- dplyr::filter(patterns, .data$pheno == "AddSex")
    if(nrow(out))
      out <- dplyr::mutate(out, pheno = pheno_names[1])
    out
  }
}
scan1_pattern <- function(pheno, phe_mx, addcovar, pairprobs_obj, K_chr, analyses_df,
                          pats, sex_type, blups) {
  analyses_df <- qtl2mediate::which_covar(analyses_df)
  wh <- match(pheno, colnames(phe_mx))
  
  addcovar <- qtl2mediate::which_covar(analyses_df, wh, addcovar)
  addcovar <- qtl2mediate::covar_matrix(addcovar)
  
  qtl2pattern::scan1pattern(pairprobs_obj$probs,
                            phe_mx[,, drop=FALSE],
                            K_chr, addcovar,
                            pairprobs_obj$map,
                            pats,
                            blups = blups)
}