afs_to_f2: Compute f2 blocks and write them to disk

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Compute f2 blocks and write them to disk

Description

This is intended for computing f2-statistics for a large number of populations, too many to do everything in working memory. It assumes that the allele frequencies have already been computed and are stored in .rds files, split into consecutive blocks for a set of populations. This function calls write_f2, which takes a (sub-)chunk of pairwise f2-statistics, and writes one pair at a time to disk.

Usage

afs_to_f2(
  afdir,
  outdir,
  chunk1,
  chunk2,
  blgsize = 0.05,
  snpwt = NULL,
  overwrite = FALSE,
  type = "f2",
  poly_only = FALSE,
  snpdat = NULL,
  apply_corr = TRUE,
  verbose = TRUE
)

Arguments

afdir	Directory with allele frequency and counts .rds files created by split_mat
outdir	Directory where data will be stored
chunk1	Index of the first chunk of populations
chunk2	Index of the second chunk of populations
blgsize	SNP block size in Morgan. Default is 0.05 (5 cM). If blgsize is 100 or greater, if will be interpreted as base pair distance rather than centimorgan distance.
snpwt	A vector of scaling factors applied to the f2-statistics for each SNP. The length has to match the number of SNPs.
overwrite	Overwrite existing files (default FALSE)
verbose	Print progress updates

See Also

extract_f2 Does the same thing in one step for smaller data.

Examples

## Not run: 
afdir = 'tmp_af_dir/'
f2dir = 'f2_dir'
extract_afs('path/to/packedancestrymap_prefix', afdir)
numchunks = length(list.files(afdir, 'afs.+rds'))
# numchunks should be the number of split allele frequency files
for(i in 1:numchunks) {
  for(j in i:numchunks) {
    afs_to_f2(afdir, f2dir, chunk1 = i, chunk2 = j)
  }
}

## End(Not run)
# Alternatively, the following code will do the same, while submitting each chunk as a separate job.
# (if \code{\link[future]{plan}} has been set up appropriately)
## Not run: 
furrr::future_map(1:numchunks, ~{i=.; map(i:numchunks, ~{
  afs_to_f2(afdir, f2dir, chunk1 = i, chunk2 = .)
  })})
  
## End(Not run)

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