f4blockdat_from_geno: f4 from genotype data
In uqrmaie1/admixtools: Inferring demographic history from genetic data

f4blockdat_from_geno

R Documentation

f4 from genotype data

Description

Compute per-block f4-statistics directly from genotype data

Usage

f4blockdat_from_geno(
  pref,
  popcombs = NULL,
  left = NULL,
  right = NULL,
  auto_only = TRUE,
  blgsize = 0.05,
  block_lengths = NULL,
  f4mode = TRUE,
  allsnps = FALSE,
  poly_only = FALSE,
  snpwt = NULL,
  keepsnps = NULL,
  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.
`left`	Populations on the left side of f4 (`pop1` and `pop2`). Can be provided together with `right` in place of `popcombs`.
`right`	Populations on the right side of f4 (`pop3` and `pop4`). Can be provided together with `left` in place of `popcombs`.
`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.
`f4mode`	If `TRUE`: f4 is computed from allele frequencies `a`, `b`, `c`, and `d` as `(a-b)(c-d)`. if `FALSE`, D-statistics are computed instead, defined as `(a-b)(c-d) / ((a + b - 2ab) * (c + d - 2cd))`, which is the same as `(P(BABA) - P(ABBA)) / (P(ABBA) + P(BABA))`.
`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.
`poly_only`	Only keep SNPs with mean allele frequency not equal to 0 or 1 (default `FALSE`).
`snpwt`	A vector of SNP weights
`keepsnps`	A vector of SNP IDs to keep
`verbose`	Print progress updates