MAF

Source: R/binom-scaling.R

Minor Allele Frequency.

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

Arguments

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.

Value

A vector of MAFs, corresponding to ind.col.

Examples

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

#>  num [1:4542] 0.342 0.206 0.237 0.185 0.456 ...