bed_counts: Counts

In bigsnpr: Analysis of Massive SNP Arrays

Counts

Description

Counts the number of 0s, 1s, 2s and NAs by variants in the bed file.

Usage

bed_counts(
  obj.bed,
  ind.row = rows_along(obj.bed),
  ind.col = cols_along(obj.bed),
  byrow = FALSE,
  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.
byrow	Whether to count by individual rather than by variant? Default is FALSE (count by variant).
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().

Value

A matrix of with 4 rows and length(ind.col) columns.

Examples

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

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

bed_counts(obj.bed, ind.row = 1:5, byrow = TRUE)

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