af: Allele frequencies

Description Usage Arguments Value Author(s) See Also

View source: R/loadaf.R

Description

Extract allele frequencies of all genomic loci from a sync object.

Usage

1
af(sync, chr, pos, repl, gen)

Arguments

sync

a sync object.

chr

character vector of chromosome names. If both chr and pos are missing (default) allele frequencies of all loci will be returned.

pos

numeric vector of sequence positions. If both chr and pos are missing (default) allele frequencies of all loci will be returned.

repl

numeric vector indicating the replicate(s).

gen

numeric vector indicating the generation(s).

Value

af returns a matrix of allele frequencies for the replicates repl and generations gen specified. Rows and columns correspond to genomic loci and replicate-generation pairs, respectively. Please note that the order of genomic loci in the sync-file is not preserved.

Author(s)

Thomas Taus

See Also

af.traj, coverage and splitLocusID.


ThomasTaus/poolSeq documentation built on Feb. 17, 2020, 1:52 p.m.