plink_to_afs: Read allele frequencies from 'PLINK' files

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Read allele frequencies from PLINK files

Description

Read allele frequencies from PLINK files

Usage

plink_to_afs(
  pref,
  inds = NULL,
  pops = NULL,
  adjust_pseudohaploid = TRUE,
  first = 1,
  last = NULL,
  numblocks = 1,
  poly_only = FALSE,
  verbose = TRUE
)

Arguments

pref	prefix of PLINK files (files have to end in .bed, .bim, .fam).
inds	Individuals from which to compute allele frequencies
pops	Populations from which to compute allele frequencies. If NULL (default), populations will be extracted from the third column in the .ind file. If population labels are provided, they should have the same length as inds, and will be matched to them by position
adjust_pseudohaploid	Genotypes of pseudohaploid samples are usually coded as 0 or 2, even though only one allele is observed. adjust_pseudohaploid ensures that the observed allele count increases only by 1 for each pseudohaploid sample. If TRUE (default), samples that don't have any genotypes coded as 1 among the first 1000 SNPs are automatically identified as pseudohaploid. This leads to slightly more accurate estimates of f-statistics. Setting this parameter to FALSE is equivalent to the ADMIXTOOLS inbreed: NO option. Setting adjust_pseudohaploid to an integer n will check the first n SNPs instead of the first 1000 SNPs.
numblocks	Number of blocks in which to read genotype file. Setting this to a number greater than one is more memory efficient, but slower.
poly_only	Only keep SNPs with mean allele frequency not equal to 0 or 1 (default FALSE).
verbose	Print progress updates

Value

A list with three items: Allele frequency matrix, allele count matrix, and SNP meta data.

Examples

## Not run: 
afdat = plink_to_afs(prefix, pops)
afs = afdat$afs
counts = afdat$counts

## End(Not run)

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