bed_MAF: Allele frequencies

In bigsnpr: Analysis of Massive SNP Arrays

Allele frequencies

Description

Allele frequencies of a bed object.

Usage

bed_MAF(
  obj.bed,
  ind.row = rows_along(obj.bed),
  ind.col = cols_along(obj.bed),
  ncores = 1
)

Arguments

obj.bed	Object of type bed, which is the mapping of some bed file. Use obj.bed <- bed(bedfile) to get this object.
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.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().

Value

A data.frame with

• ⁠$ac⁠: allele counts,

• ⁠$mac⁠: minor allele counts,

• ⁠$af⁠: allele frequencies,

• ⁠$maf⁠: minor allele frequencies,

• ⁠$N⁠: numbers of non-missing values.

Examples

bedfile <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
obj.bed <- bed(bedfile)

bed_MAF(obj.bed, ind.col = 1:5)

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.