#' Check MAF
#'
#' Check Minor Allele Frequency (MAF) column is
#' prepared for running \pkg{coloc}. Must be numeric, <1, >0,
#' and not contain NAs.
#' @param verbose Print messages.
#' @keywords internal
check_maf <- function(gwas_shared,
eqtl_shared,
verbose=TRUE) {
MAF <- maf.QTL <- NULL;
if (!"MAF" %in% colnames(gwas_shared)) {
messager(
"WARNING: `MAF` column not provided in GWAS data.",
"Borrowing MAF from QTL data instead.",v=verbose
)
gwas_shared$MAF <- eqtl_shared$maf.QTL
}
#### Ensure MAF is within expected range ####
## gwas_shared
gwas_shared$MAF <- as.numeric(gwas_shared$MAF)
gwas_shared <- subset(
gwas_shared,
MAF > 0 & MAF < 1 & (!is.na(MAF))
)
## eqtl_shared
eqtl_shared$maf.QTL <- as.numeric(eqtl_shared$maf.QTL)
eqtl_shared <- subset(
eqtl_shared,
maf.QTL > 0 & maf.QTL < 1 & (!is.na(maf.QTL))
)
return(list(
gwas_shared = gwas_shared,
eqtl_shared = eqtl_shared
))
}
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