forcePool {poolHelper}

Randomly select the required number of loci from the pooled sequencing data

Description

This function removes loci without polymorphic sites and then randomly selects the required number of loci from a larger dataset.

Usage

forcePool(nSims, pool, target)

Arguments

nSims

is an integer representing how many types of simulations were performed. The possible types of simulations include loci without barriers against migration between divergent ecotypes, loci without migration from the C towards the W ecotype, loci without migration from the W towards the C ecotypes and loci where no migration occurs between divergent ecotypes.

pool

a list containing the "minor" element, representing the number of reads with the minor-allele and the "total" element that contains information about the total number of Reads. The list should also contain a "major" entry with the information about reads containing the major-allele.

target

is a vector with the required number of loci per category. If extra loci were simulated, this vector informs how many loci of each simulation type should be randomly selected.

Details

If extra loci were simulated to try to have sufficient loci to keep the required number of loci after filtering, then this function is used to remove extra loci. This is done by randomly selecting the required number of loci from the full contingent of extra simulated loci.

Value

a list with three named entries

major

a list with one entry per locus. Each entry is a matrix with the number of major allele reads for each population. Each column represents a different site and each row a different population.

minor

a list with one entry per locus. Each entry is a matrix with the number of minor allele reads for each population. Each column represents a different site and each row a different population.

total

a list with one entry per locus. Each entry is a matrix with the coverage of each population. Each column represents a different site and each row a different population.