discardSnpsLowMaf: Minor allele frequencies

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Minor allele frequencies

Description

Discard the SNPs with a minor allele frequency below the given threshold, as well as monomorphic SNPs.

Usage

discardSnpsLowMaf(X, mafs = NULL, thresh = 0.01, rmv.mono = FALSE, verbose = 1)

Arguments

X	matrix of bi-allelic SNP genotypes encoded in allele doses in [0,2], with genotypes in rows and SNPs in columns; missing values should be encoded as NA
mafs	vector of minor allele frequencies; if NULL, will be estimated with estimSnpMaf
thresh	threshold on minor allele frequencies strictly below which SNPs are ignored
rmv.mono	if TRUE, monomorphic SNPs are also removed
verbose	verbosity level (0/1)

Value

matrix similar to X but possibly with less columns

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.