estimSnpAf: Allele frequencies

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

Allele frequencies

Description

Estimate allele frequencies of bi-allelic SNPs. If previous sample sizes and counts per SNP are provided, it updates them.

Usage

estimSnpAf(
  X,
  allow.updating = FALSE,
  prev.nb.genos = NULL,
  prev.nb.refalls = NULL
)

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
allow.updating	if TRUE, the sample sizes and counts per SNP will be kept to allow further updating
prev.nb.genos	vector of number of genotypes (sample sizes per SNP); the length and names should correspond to the columns of the X matrix
prev.nb.refalls	vector of number of reference alleles (counts per SNP); the length and names should correspond to the columns of the X matrix

Value

vector, with sample sizes and counts per SNP as attributes if updating is allowed

Author(s)

Timothee Flutre

See Also

estimSnpMaf

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