calculateAlleleFreq: XIBD Calculate Population Allele Frequencies

In bahlolab/XIBD: Identity-by-Descent Analysis of the Human Genome

Description

Calculate population allele frequencies from genotypes.

Usage

calculateAlleleFreq(ped.genotypes)

Arguments

ped.genotypes

a named list containing pedigree, genotypes and model. See Value description in getGenotypes for more details.

Value

a data frame with information:

1. Chromosome (type "character", "numeric" or "integer")

2. SNP identifiers (type "character")

3. Genetic map distance (Morgans, M) (type "numeric")

4. Base-pair position (type "numeric" or "integer")

5. Population allele frequency (type "numeric")

where each row defines a unique SNP. Allele frequencies of -1 indicate missing data for all samples for that SNP.

bahlolab/XIBD documentation built on May 11, 2019, 5:24 p.m.