remove_by_reads {poolHelper}

Apply a coverage-based filter over a list

Description

This function removes sites that have a coverage below a minimum value and sites with a coverage above a maximum value. This is done over multiple loci, assuming that each entry of the reads list is a different locus. If a list of genotypes is also supplied, then those same sites are also removed from each locus of the genotypes.

Usage

remove_by_reads(nLoci, reads, minimum, maximum, genotypes = NA)

Arguments

nLoci

an integer that represents how many independent loci were simulated.

reads

a list with the total depth of coverage. Each entry of the list should be a matrix corresponding to a different locus. Each row of that 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 list input with the genotypes. Each entry of the list should be a matrix corresponding to a different locus. Each column of the matrix should be a different site and each row a different individual.

Value

a list with the total depth of coverage similar to the reads input argument but without sites where the coverage was below the minimum or above the maximum. If the genotypes were included, a second list entry will also be included in the output, containing the genotypes minus the sites that were removed.

Examples

set.seed(10)

# simulate coverage for 10 locus
reads <- simulateCoverage(mean = c(25, 25), variance = c(200, 200), nSNPs = 10, nLoci = 10)

# remove sites with coverage below 10x or above 100x
reads <- remove_by_reads(nLoci = 10, reads = reads, minimum = 5, maximum = 100)
# notice that some locus no longer have 10 SNPs - those sites were removed
reads