snp_split: Split-parApply-Combine

Description

A Split-Apply-Combine strategy to parallelize the evaluation of a function on each SNP, independently.

snp_split(infos.chr, FUN, combine, ncores = 1, ...)

infos.chr: Vector of integers specifying each SNP's chromosome.
Typically <bigSNP>$map$chromosome.
FUN: The function to be applied. It must take a FBM.code256 as first argument and ind.chr, an another argument to provide subsetting over SNPs. You can access the number of the chromosome by using attr(ind.chr, "chr").
combine: function that is used by foreach::foreach to process the tasks results as they generated. This can be specified as either a function or a non-empty character string naming the function. Specifying 'c' is useful for concatenating the results into a vector, for example. The values 'cbind' and 'rbind' can combine vectors into a matrix. The values '+' and '*' can be used to process numeric data. By default, the results are returned in a list.
ncores: Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().
...: Extra arguments to be passed to FUN.

This function splits indices for each chromosome, then apply a given function to each part (chromosome) and finally combine the results.

# parallelize over chromosomes made easy
# examples of functions from this package
snp_pruning
snp_clumping
snp_fastImpute

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