snp_split: Split-parApply-Combine

In bigsnpr: Analysis of Massive SNP Arrays

Split-parApply-Combine

Description

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

Usage

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

Arguments

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.

Details

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

Value

The result of foreach::foreach.

Examples

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

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.