f3blockdat_from_geno: f3 from genotype data
In uqrmaie1/admixtools: Inferring demographic history from genetic data

f3blockdat_from_geno

R Documentation

f3 from genotype data

Description

Compute per-block f3-statistics directly from genotype data

Usage

f3blockdat_from_geno(
  pref,
  popcombs,
  auto_only = TRUE,
  blgsize = 0.05,
  block_lengths = NULL,
  allsnps = FALSE,
  adjust_pseudohaploid = TRUE,
  poly_only = FALSE,
  apply_corr = TRUE,
  outgroupmode = FALSE,
  verbose = TRUE
)

Arguments

`pref`	Prefix of genotype files
`popcombs`	A data frame with one population combination per row, and columns `pop1`, `pop2`, `pop3`, `pop4`. If there is an additional integer column named `model` and `allsnps = FALSE`, only SNPs present in every population in any given model will be used to compute f4-statistics for that model.
`auto_only`	Use only chromosomes 1 to 22.
`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.
`block_lengths`	An optional vector with block lengths. If `NULL`, block lengths will be computed.
`allsnps`	Use all SNPs with allele frequency estimates in every population of any given population quadruple. If `FALSE` (the default) only SNPs which are present in all populations in `popcombs` (or any given model in it) will be used. Setting `allsnps = TRUE` in the presence of large amounts of missing data might lead to false positive results.
`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.
`apply_corr`	With `apply_corr = FALSE`, no bias correction is performed. With `apply_corr = TRUE` (the default), a bias correction term based on the heterozygosity in the first population is subtracted from the f3 estimate. With `apply_corr = 2`, the bias correction term is calculated based on all 3 populations. This option is not generally recommended, and only exists to match how the f3-statistics are estimated in certain scenarios in the original qpGraph program.
`outgroupmode`	With `outgroupmode = FALSE`, estimates of f3 will be normalized by estimates of the heterozygosity of the target population. This is the default option if the first argument is the prefix of genotype data. If the first argument is an array of precomputed f2-statistics, then no normalization can be performed, which corresponds to `outgroupmode = TRUE`.
`verbose`	Print progress updates