read_Q_matrix: Read ancestry proportions ('Q-matrix') from ADMIXTURE run

In andrewparkermorgan/popcorn: File-Format Wrangler for Population-Based Genetic Data

Read ancestry proportions ('Q-matrix') from ADMIXTURE run

Description

Read ancestry proportions ('Q-matrix') from ADMIXTURE run

Usage

read_Q_matrix(infile, K = NULL, iids = NULL, ...)

Arguments

infile	path to matrix of ancestry proportions (*.Q file) from ADMIXTURE run
K	number of clusters; if NULL (default), attempt to infer from filename
iids	sample IDs (in same order as rows in matrix); if NULL (default), look for corresponding *.fam file
...	extra arguments, ignored

Details

If K and iids are both NULL (default), assumes that estimation was performed from a PLINK *.bed file, and that the corresponding *.fam file resides in same directory as output. If standard errors for ancestrty proportions are availbale (*.Q_se file), they are read as well and stored in attr(result, "se").

andrewparkermorgan/popcorn documentation built on July 8, 2023, 12:42 p.m.