filterPool: Filter Pool-seq data according to a minor-allele reads...

In poolHelper: Simulates Pooled Sequencing Genetic Data

Filter Pool-seq data according to a minor-allele reads threshold

Description

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

Usage

filterPool(pool, nloci, min.minor)

Arguments

pool	a list containing the "reference" element, representing the number of reads with the reference allele, the "alternative" element representing the number of reads with the alternative allele and the "total" element that contains information about the total number of reads.
nloci	an integer that represents the total number of independent loci in the dataset.
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.