f2_from_geno: Compute blocked f2 statistics

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Compute blocked f2 statistics

Description

This function prepares data for various other ADMIXTOOLS 2 functions. It reads data from genotype files, computes allele frequencies and blocked f2-statistics for selected populations, and returns them as a 3d array.

Usage

f2_from_geno(
  pref,
  inds = NULL,
  pops = NULL,
  blgsize = 0.05,
  maxmem = 8000,
  maxmiss = 0,
  minmaf = 0,
  maxmaf = 0.5,
  pops2 = NULL,
  outpop = NULL,
  outpop_scale = TRUE,
  transitions = TRUE,
  transversions = TRUE,
  auto_only = TRUE,
  keepsnps = NULL,
  afprod = FALSE,
  fst = FALSE,
  poly_only = c("f2"),
  format = NULL,
  adjust_pseudohaploid = TRUE,
  remove_na = TRUE,
  apply_corr = TRUE,
  qpfstats = FALSE,
  verbose = TRUE,
  ...
)

Arguments

pref	Prefix of PLINK/EIGENSTRAT/PACKEDANCESTRYMAP files. EIGENSTRAT/PACKEDANCESTRYMAP have to end in .geno, .snp, .ind, PLINK has to end in .bed, .bim, .fam
inds	Individuals for which data should be extracted
pops	Populations for which data should be extracted. If both pops and inds are provided, they should have the same length and will be matched by position. If only pops is provided, all individuals from the .ind or .fam file in those populations will be extracted. If only inds is provided, each indivdual will be assigned to its own population of the same name. If neither pops nor inds is provided, all individuals and populations in the .ind or .fam file will be extracted.
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.
maxmem	Maximum amount of memory to be used. If the required amount of memory exceeds maxmem, allele frequency data will be split into blocks, and the computation will be performed separately on each block pair. This doesn't put a precise cap on the amount of memory used (it used to at some point). Set this parameter to lower values if you run out of memory while running this function. Set it to higher values if this function is too slow and you have lots of memory.
maxmiss	Discard SNPs which are missing in a fraction of populations higher than maxmiss
minmaf	Discard SNPs with minor allele frequency less than minmaf
maxmaf	Discard SNPs with minor allele frequency greater than than maxmaf
pops2	If specified, only a pairs between pops and pops2 will be computed
outpop	Keep only SNPs which are heterozygous in this population
outpop_scale	Scale f2-statistics by the inverse outpop heteroygosity (1/(p*(1-p))). Providing outpop and setting outpop_scale to TRUE will give the same results as the original qpGraph when the outpop parameter has been set, but it has the disadvantage of treating one population different from the others. This may limit the use of these f2-statistics for other models.
transitions	Set this to FALSE to exclude transition SNPs
transversions	Set this to FALSE to exclude transversion SNPs
auto_only	Keep only SNPs on chromosomes 1 to 22
keepsnps	SNP IDs of SNPs to keep. Overrides other SNP filtering options
afprod	Return negative average allele frequency products instead of f2-statistics. Setting afprod = TRUE will result in more precise f4-statistics when the original data had large amounts of missingness, and should be used in that case for qpdstat and qpadm. It can also be used for outgroup f3-statistics with a fixed outgroup (for example for qpgraph); values will be shifted by a constant amount compared to regular f3-statistics. This shift affects the fit of a graph only by small amounts, possibly less than bias in regular f3-statistics introduced by large amounts of missing data.
fst	Write files with pairwise FST for every population pair. Setting this to FALSE can make extract_f2 faster and will require less memory.
poly_only	Specify whether SNPs with identical allele frequencies in every population should be discarded (poly_only = TRUE), or whether they should be used (poly_only = FALSE). By default (poly_only = c("f2")), these SNPs will be used to compute FST and allele frequency products, but not to compute f2 (this is the default option in the original ADMIXTOOLS).
format	Supply this if the prefix can refer to genotype data in different formats and you want to choose which one to read. Should be plink to read .bed, .bim, .fam files, or eigenstrat, or packedancestrymap to read .geno, .snp, .ind files.
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 treats all samples as diploid and 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	Apply small-sample-size correction when computing f2-statistics (default TRUE)
qpfstats	Compute smoothed f2-statistics (default FALSE). In the presence of large amounts of missing data, this option can be used to retain information from all SNPs while introducing less bias than setting maxmiss to values greater than 0. When setting qpfstats = TRUE, most other options to extract_f2 will be ignored. See qpfstats for more information. Arguments to qpfstats can be passed via ...
verbose	Print progress updates
...	Pass arguments to qpfstats

Value

A 3d array of f2-statistics (or scaled allele frequency products if afprod = TRUE)

See Also

f2_from_precomp for reading previously stored f2-statistics into R, extract_f2 for storing f2-statistics on disk

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