Allele frequencies — bed

Allele frequencies of a bed object.

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)
#>   ac mac         af        maf   N
#> 1  8   8 0.02094241 0.02094241 191
#> 2 16  16 0.04145078 0.04145078 193
#> 3 23  23 0.05989583 0.05989583 192
#> 4 34  34 0.08717949 0.08717949 195
#> 5 43  43 0.10969388 0.10969388 196