snprelate_allele_frequencies {snplinkage}

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.