kinship.plink: Compute realized kinship matrix (aka GRM) with PLINK

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Compute realized kinship matrix (aka GRM) with PLINK

Usage

kinship.plink(prefix, method = "--distance square 1-ibs", flags = "",
  prune = FALSE, ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
method	command-line flags for PLINK, controlling underlying calculation
flags	command-line flags passed directly to underlying PLINK call
prune	logical; if TRUE, do a round of LD-pruning before calculating kinship matrix
...	ignored

Details

See the relevant PLINK documentation for details of the underlying calculations. The default is to compute the 'Mahnattan distance' between samples, ie. 1 minus the mean number alleles shared identical-by-state across all markers.

Value

a square matrix of genetic distances (or similarities), with row and column names equal to the sample IDs

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.