calculatePi {poolHelper}

Calculate population frequency at each SNP

Description

The frequency at a given SNP is calculated according to: pi = c/r, where c = number of minor-allele reads and r = total number of observed reads.

Usage

calculatePi(listPool, nLoci)

Arguments

listPool

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. The output of the poolPops function should be used as input here.

nLoci

an integer that represents the total number of independent loci in the dataset.

Details

This function takes as input a list that contains the number of reads with the minor allele and the number of total reads per population at a given site. The names of the respective elements of the list should be minor and total. It works with lists containing just one set of minor and total reads, corresponding to a single locus, and with lists where each entry contains a different set of minor and total number of reads, corresponding to different loci.

Value

a list with two named entries

pi

a list with the allele frequencies of each population. Each list entry is a matrix, corresponding to a different locus. Each row of a matrix corresponds to a different population and each column to a different site.

pool

a list with three different entries: major, minor and total. This list is similar to the one obtained with the findMinor function.

Examples

# simulate coverage at 5 SNPs for two populations, assuming 20x mean coverage
reads <- simulateCoverage(mean = c(20, 20), variance = c(100, 100), nSNPs = 5, nLoci = 1)

# simulate the number of reads contributed by each individual
# for each population there are two pools, each with 5 individuals
indContribution <- popsReads(list_np = rep(list(rep(5, 2)), 2), coverage = reads, pError = 5)

# set seed and create a random matrix of genotypes for the 20 individuals - 10 per population
set.seed(10)
genotypes <- matrix(rpois(100, 0.5), nrow = 20)

# simulate the number of reference reads for the two populations
readsReference <- numberReferencePop(genotypes = genotypes, indContribution = indContribution,
size = rep(list(rep(5, 2)), 2), error = 0.01)

# create Pooled DNA sequencing data for these two populations and for a single locus
pools <- poolPops(nPops = 2, nLoci = 1, indContribution = indContribution,
readsReference = readsReference)

# define the major and minor alleles for this pool-seq data
# note that we have to select the first entry of the pools list
# because this function works for matrices
pools <- findMinor(reference = pools$reference[[1]], alternative = pools$alternative[[1]],
coverage = pools$total[[1]])

# calculate population frequency at each SNP of this locus
calculatePi(listPool = pools, nLoci = 1)