gt_extract_f2.RdThis function prepares data for various ADMIXTOOLS 2 functions fro the
package ADMIXTOOLS 2. It
takes a gen_tibble,
computes allele frequencies and blocked f2-statistics,
and writes the results to outdir. It is equivalent to
admixtools::extract_f2().
gt_extract_f2(
.x,
outdir = NULL,
blgsize = 0.05,
maxmem = 8000,
maxmiss = 0,
minmaf = 0,
maxmaf = 0.5,
minac2 = FALSE,
outpop = NULL,
outpop_scale = TRUE,
transitions = TRUE,
transversions = TRUE,
overwrite = FALSE,
adjust_pseudohaploid = TRUE,
fst = TRUE,
afprod = TRUE,
poly_only = c("f2"),
apply_corr = TRUE,
n_cores = 1,
quiet = FALSE
)Directory where data will be stored.
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.
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.
Discard SNPs which are missing in a fraction of populations
higher than maxmiss
Discard SNPs with minor allele frequency less than minmaf
Discard SNPs with minor allele frequency greater than
than maxmaf
Discard SNPs with allele count lower than 2 in any population
(default FALSE). This option should be set to TRUE when computing
f3-statistics where one population consists mostly of pseudohaploid samples.
Otherwise heterozygosity estimates and thus f3-estimates can be biased.
minac2 == 2 will discard SNPs with allele count lower than 2 in any
non-singleton population (this option is experimental and is based on the
hypothesis that using SNPs with allele count lower than 2 only leads to
biases in non-singleton populations). Note that, While the minac2 option
discards
SNPs with allele count lower than 2 in any population, the qp3pop
function will only discard SNPs with allele count lower than 2 in the
first (target) population (when the first argument is the prefix of
a genotype file; i.e. it is applied directly to a genotype file, not via
precomputing f2 from a gen_tibble).
Keep only SNPs which are heterozygous in this population
Scale f2-statistics by the inverse outpop
heterozygosity (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.
Set this to FALSE to exclude transition SNPs
Set this to FALSE to exclude transversion SNPs
Overwrite existing files in outdir
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.
Write files with pairwise FST for every population pair.
Setting this to FALSE can make extract_f2 faster and will require less memory.
Write files with allele frequency products for every
population pair. Setting this to FALSE can make extract_f2 faster and
will require less memory.
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).
Apply small-sample-size correction when computing
f2-statistics (default TRUE)
Parallelize computation across n_cores cores.
Suppress printing of progress updates
SNP metadata (invisibly)