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

Usage

readSnpsPed(pedfile, mapfile)

Arguments

pedfile: A dataframe dataframe generated from mrvip function
mapfile: A dataframe response dataset

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("bobcat.plink.ped", "bobcat.plink.map.map") #NAs in data and interpolated as the mode. 
X <- filterRareCommon (snps, lower=0.4, higher=0.7) #these are harsh # \dontrun{}
#> Error in eval(expr, envir, enclos): object 'snps' not found