afs_to_f2_blocks: Compute all pairwise f2 statistics

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Compute all pairwise f2 statistics

Description

This function takes a allele frequency data and computes blocked f2 statistics for all population pairs, which are written to outdir. f2 for each SNP is computed as (p1 - p2)^2 - p1 (1 - p1)/(n1 - 1) - p2 (1 - p2)/(n2 - 1), where p1 and p2 are allele frequencies in populations 1 and 2, and n1 and n2 is the number of non-missing haplotypes in populations 1 and 2. See details

Usage

afs_to_f2_blocks(
  afdat,
  maxmem = 8000,
  blgsize = 0.05,
  pops1 = NULL,
  pops2 = NULL,
  outpop = NULL,
  outdir = NULL,
  overwrite = FALSE,
  afprod = TRUE,
  fst = TRUE,
  poly_only = c("f2"),
  apply_corr = apply_corr,
  n_cores = 1,
  verbose = TRUE
)

Arguments

afdat	A list with three items with the same SNP in each row (generated by packedancestrymap_to_afs or plink_to_afs) afs A matrix of allele frequencies for all populations (columns) and SNPs (rows) counts A matrix of allele counts for all populations (columns) and SNPs (rows) snpdat A data frame with SNP metadata
maxmem	split up allele frequency data into blocks, if memory requirements exceed maxmem MB.
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.
outpop	If specified, f2-statistics will be weighted by heterozygosity in this population
outdir	Directory into which to write f2 data (if NULL, data is returned instead)
overwrite	Should existing files be overwritten? Only relevant if outdir is not NULL
poly_only	Exclude sites with identical allele frequencies in all populations. Can be different for f2-statistics, allele frequency products, and fst. Should be a character vector of length three, with some subset of c("f2", "ap", "fst")
verbose	Print progress updates
pop1	pops1 and pops2 can be specified if only a subset of pairs should be computed.
pop2	pops1 and pops2 can be specified if only a subset of pairs should be computed.

Details

For each population pair, each of the i = 1, \ldots, n resutling values (n is around 700 in practice) is the mean f2 estimate across all SNPs except the ones in block i.

- p1 (1 - p1)/(2 n1 - 1) - p2 (1 - p2)/(2 n2 - 1) is a correction term which makes the estimates unbiased at low sample sizes.

Examples

## Not run: 
afdat = plink_to_afs('/my/geno/prefix')
afs_to_f2_blocks(afdat, outdir = '/my/f2/data/')

## End(Not run)

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