read_sfs: Read 'flattened' site frequency spectrum (SFS) from a file

In andrewparkermorgan/sfsr: Utilities for Manipulating Allele Frequency Spectra

Description

Read 'flattened' site frequency spectrum (SFS) from a file

Usage

read_sfs(ff, dims, dtype = double, bootstraps = TRUE, repolarize = FALSE,
  ...)

Arguments

ff	filename
dims	sample sizes (number of chromosomes) along each dimension of SFS
dtype	what sort of frequences to expect; best let the procedure auto-detect
bootstraps	logical; if TRUE, read bootstrap replicates (one per line) if they are present
repolarize	logical; if TRUE, swap ancestral and derived states (see Details)
...	ignored

Details

The SFS is expected to be provided in a text file as space-separated numbers (integers or floating-point), in row-major order. An unfolded SFS (ie. polarized against the derived allele) is expected, although this may be relaxed in future

NB: Recent versions of ANGSD apparently get the ancestral and derived alleles backwards. Use repolarize = TRUE to correct this issue at runtime.

Value

a site frequency spectrum (SFS): a k-dimensional array representing the joint frequencies of derived alleles in each of k populations

andrewparkermorgan/sfsr documentation built on May 10, 2019, 11:10 a.m.