snprelate_allele_frequencies: Compute allele frequencie and snp missing rate

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Compute allele frequencie and snp missing rate

Description

Wrapper over SNPRelate::snpgdsSNPRateFreq

Usage

snprelate_allele_frequencies(
  gdata,
  snps_idx = NULL,
  scans_idx = NULL,
  quiet = FALSE
)

Arguments

gdata	A GenotypeData object
snps_idx	Vector of snps indices
scans_idx	Vector of scans indices
quiet	Whether to be quiet

Value

A data frame of snps_idx, snps_ids, allele1, allele2, maf, missing where allele1 and allele2 are the rates of the alleles, and maf the minimum of the 2. Missing is the missing rate. N.B: the allele rates are computed on the non missing genotypes, i.e. their sum equals 1.

snplinkage documentation built on May 4, 2023, 9:09 a.m.