filterMinor: Filter sites according to a minor-allele reads threshold

In poolHelper: Simulates Pooled Sequencing Genetic Data

Filter sites according to a minor-allele reads threshold

Description

Removes sites from matrices with counts of reads. If a site has less minor-allele reads than min.minor across all populations, that site is removed from the data.

Usage

filterMinor(reference, alternative, coverage, min.minor)

Arguments

reference	a matrix with the number of reads with the reference allele. Each row should be a different population and each column a different site.
alternative	a matrix with the number of reads with the alternative allele. Each row should be a different population and each column a different site.
coverage	is a matrix of total coverage. Each row of the matrix should be a different population and each column a different site. Thus, each entry of the matrix contains the total number of observed reads for that population at a given site.
min.minor	is an integer representing the minimum allowed number of minor-allele reads. Sites that, across all populations, have less minor-allele reads than this threshold will be removed from the data.

Value

a list with three named entries:

reference	a list with one entry per locus. Each entry is a matrix with the number of reference allele reads. Each column represents a different site.
alternative	a list with one entry per locus. Each entry is a matrix with the number of alternative allele reads. Each column represents a different site.
total	a list with one entry per locus. Each entry is a matrix with the total depth of coverage. Each column represents a different site.

poolHelper documentation built on July 9, 2023, 6:23 p.m.