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maf.md

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NAME

compute_MAF

USAGE

compute_MAF(snpdata, include.het=FALSE, mat.name="GT")

DESCRIPTION

compute_MAF is a function that calculates the minor allele frequency (MAF) for every locus from the specified genotype table specified in mat.name argument ("GT": calculate MAF from the raw data; "Phased": calculate MAF from the phased data; "Imputed": calculate MAF from the imputed data). When include.het=TRUE, the mixed genotypes will be considered in the MAF calculation

OPTIONS

snpdata: an object of class SNPdata
include.het: whether to account for mixed genotypes or not
mat.name: the genotype matrix from which MAF will be calculated

RETURN

a SNPdata object with 2 additional columns in the details data frame:

     1.  MAF: the minor allele frequency
     2.  MAF_allele: the least frequent allele