coverage: Sequence coverages

In ThomasTaus/poolSeq: Simulate and Analyze Pool-seq Data

Description

Extract sequence coverages of all genomic loci from a sync object.

Usage

coverage(sync, chr, pos, repl, gen)

Arguments

sync	a sync object.
chr	character vector of chromosome names. If both chr and pos are missing (default) sequence coverages of all loci will be returned.
pos	numeric vector of sequence positions. If both chr and pos are missing (default) sequence coverages of all loci will be returned.
repl	numeric vector indicating the replicate(s).
gen	numeric vector indicating the generation(s).

Value

coverage returns a matrix of sequence coverages 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, af.traj and splitLocusID.

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