twoway: Get two-way (marker x marker)-phenotype association

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

Description

Get two-way (marker x marker)-phenotype association

Usage

twoway(gty, markers, verbose = TRUE, ...)

Arguments

gty	a genotypes object
markers	indexing vector into gty: can be logical, character or numeric
verbose	logical; if TRUE, preview the contingency table on the console
...	ignored

Details

A wrapper around oneway(), generalizing it to marker pairs. The contingency table built from the result of twoway() will be (genotype x genotype) instead of (genotype x phenotype), so the phenotype must be summarizeable. This function recodes binary phenotypes to 0=control/1=case so that taking the mean gives a penetrance value. Other ordinal or categorical phenotypes will be converted from factor to the underlying integer representation, which may or may not be meaningful.

Value

a dataframe with marker metadata, genotype calls, and sample metadata including phenotype

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