alleles: Allelic information

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

Description

Extract allelic information, such as reference, minor, major and rising allele, of all genomic loci from a sync object.

Usage

alleles(sync, chr, pos)

Arguments

sync	a sync object.
chr	character vector of chromosome names. If both chr and pos are missing (default) allelic information of all loci will be returned.
pos	numeric vector of sequence positions. If both chr and pos are missing (default) allelic information of all loci will be returned.

Value

alleles returns a data.table containing information for each genomic locus in sync. Please note that the order of genomic loci in the sync-file is not preserved. The returned data.table provides the following columns:

chr	chromosome name.
pos	sequence position.
ref	reference allele.
major	major allele.
minor	minor allele.
rising	rising allele.

Author(s)

Thomas Taus

See Also

polarization, af and af.traj.

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