group_samples: Group precomputed data

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Group precomputed data

Description

Computing f2 statistics for populations consisting of many individuals can be slow and require a lot of memory. To speed this up, this function groups individuals into populations, computes allele counts and products of pairwise allele counts with all individuals and groups, and writes the data to disk. f2 statistics for a combination of grouped and ungrouped precomputed data can then be read using f2_from_precomp, replacing individual IDs of the grouped samples with the new group labels. All groupings are listed in ⁠{dir}/groups/{groupname}.rds⁠

Usage

group_samples(dir, inds, pops, overwrite = FALSE, verbose = TRUE)

Arguments

dir	Directory with precomputed individual pair data
inds	Individuals to group
pops	Group names, either length 1, or same length as inds
overwrite	Overwrite existing files in outdir
verbose	print progress updates

See Also

delete_groups

Examples

## Not run: 
dir = 'my/f2/dir/'
inds = c('ind1', 'ind2', 'ind3', 'ind4', 'ind5')
pops = c('pop_A', 'pop_A', 'pop_A', 'pop_B', 'pop_B')
group_samples(dir, inds, pops)

## End(Not run)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.