Compute count blocks and write them to disk

Source: R/io.R

This is intended for computing allele count data for a large number of individuals, 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 individuals.

afs_to_counts(
  genodir,
  outdir,
  chunk1,
  chunk2,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

genodir

Directory with genotype files split in chunks created by extract_afs (with each individual its own population).

outdir

Directory where allele count data will be stored

chunk1

Index of the first chunk of individuals

chunk2

Index of the second chunk of individuals

overwrite

Overwrite existing files (default FALSE)

verbose

Print progress updates

See also

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