bigsnpr: bed_MAF – R documentation

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bed_MAF

Allele frequencies

Allele frequencies of a bed object.

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

`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 nb_cores.

A data.frame with

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

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

Analysis of Massive SNP Arrays

v1.10.8

GPL-3

Authors

Florian Privé [aut, cre], Michael Blum [ths], Hugues Aschard [ths], Bjarni Jóhann Vilhjálmsson [ths]

Initial release

2022-07-05