Minor Allele Frequency.
snp_MAF(
G,
ind.row = rows_along(G),
ind.col = cols_along(G),
nploidy = 2,
ncores = 1
)
A FBM.code256
(typically <bigSNP>$genotypes
).
You shouldn't have missing values. Also, remember to do quality control,
e.g. some algorithms in this package won't work if you use SNPs with 0 MAF.
An optional vector of the row indices (individuals) that
are used. If not specified, all rows are used.
Don't use negative indices.
An optional vector of the column indices (SNPs) that are used.
If not specified, all columns are used.
Don't use negative indices.
Number of trials, parameter of the binomial distribution.
Default is 2
, which corresponds to diploidy, such as for the human genome.
Number of cores used. Default doesn't use parallelism.
You may use bigstatsr::nb_cores()
.
A vector of MAFs, corresponding to ind.col
.
obj.bigsnp <- snp_attachExtdata()
str(maf <- snp_MAF(obj.bigsnp$genotypes))
#> num [1:4542] 0.342 0.206 0.237 0.185 0.456 ...