bigsnpr: snp_MAF – R documentation

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snp_MAF

MAF

Minor Allele Frequency.

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

`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 nb_cores.

A vector of MAFs, corresponding to ind.col.

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

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