Conversion to single column per locus from plink file via LEA functionality

Usage

readSnpsPed(pedfile, mapfile)

Arguments

pedfile: A file location.
mapfile: A file location.

Value

A tibble.

Details

Function to import SNP data from a plink format into a format suitable for MrIML predicts (presence/absence of an alelle for each locus). Currently if there is missing data (NAs) it either imputes them as the mode or leaves them. A histogram is also produced of the missing data.

Examples

if (FALSE) {
snps <- readSnpsPed("FILE_NAME.plink.ped", "FILE_NAME.plink.map.map")
X <- filterRareCommon(snps, lower = 0.4, higher = 0.7) 
}