snp_MAF: MAF

In bigsnpr: Analysis of Massive SNP Arrays

MAF

Description

Minor Allele Frequency.

Usage

snp_MAF(
  G,
  ind.row = rows_along(G),
  ind.col = cols_along(G),
  nploidy = 2,
  ncores = 1
)

Arguments

G	A FBM.code256 (typically ⁠<bigSNP>$genotypes⁠). You shouldn't have missing values. Also, remember to do quality control, e.g. some algorithms in this package won't work if you use SNPs with 0 MAF.
ind.row	An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices.
ind.col	An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used. Don't use negative indices.
nploidy	Number of trials, parameter of the binomial distribution. Default is 2, which corresponds to diploidy, such as for the human genome.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().

Value

A vector of MAFs, corresponding to ind.col.

Examples

obj.bigsnp <- snp_attachExtdata()
str(maf <- snp_MAF(obj.bigsnp$genotypes))

bigsnpr documentation built on April 4, 2025, 12:20 a.m.