remove_by_reads_matrix {poolHelper}

Apply a coverage-based filter to a matrix

Description

This function removes sites that have a coverage below a minimum value and sites with a coverage above a maximum value. If a matrix of genotypes is also supplied, then those same sites are also removed from that matrix.

Usage

remove_by_reads_matrix(reads, minimum, maximum, genotypes = NA)

Arguments

reads

a matrix with the total depth of coverage. Each row of the matrix should be the coverage of a different population and each column a different site.

minimum

an integer representing the minimum coverage allowed. Sites where any population has a depth of coverage below this threshold are removed from the data.

maximum

an integer representing the maximum coverage allowed. Sites where any population has a depth of coverage above this threshold are removed from the data.

genotypes

an optional matrix input with the genotypes. Each column of the matrix should be a different site and each row a different individual.

Value

a matrix with the total depth of coverage minus the sites (i.e. columns) where the coverage for any of the populations was below the minimum or above the maximum. If genotypes were supplied, then the output will be a list, with one entry per locus. Each entry will contain the filtered coverage in the first entry and the genotypes, minus the removed sites, in the second entry.

Examples

set.seed(10)

# simulate coverage for a single locus - select the first entry to obtain a matrix
reads <- simulateCoverage(mean = c(25, 25), variance = c(200, 200), nSNPs = 10, nLoci = 1)[[1]]

# check the coverage matrix
reads

# remove sites with coverage below 10x or above 100x
remove_by_reads_matrix(reads = reads, minimum = 10, maximum = 100)