computeReference {poolHelper}

Compute the number of reference reads over a matrix

Description

This function works over all the rows and columns of a matrix and computes the number of reads containing the reference allele at each site and for each individual.

Usage

computeReference(genotypes, indContribution, error)

Arguments

genotypes

is a matrix of genotypes. Each column of the matrix should be a different site and each row a different individual. Genotypes should be encoded as 0: reference homozygote, 1: heterozygote and 2: alternative homozygote.

indContribution

is a matrix of individual contributions. Each row of that matrix is a different individual and each column is a different site. Thus, each entry of the matrix should contain the number of reads contributed by that individual at that particular site.

error

a numeric value with error rate associated with the sequencing and mapping process. This error rate is assumed to be symmetric: error(reference -> alternative) = error(alternative -> reference). This number should be between 0 and 1.

Value

a matrix with the number of reference allele reads contributed by each individual. Each row of the matrix represents a different individual and each column is a different site.

Examples

# probability of contribution for 10 individuals at 5 sites
probs <- indProbs(np = 10, nSNPs = 5, pError = 5)

# simulate the number of reads contributed, assuming 20 coverage for each site
indContribution <- indReads(np = 10, coverage = rep(20, 5), probs = probs)

# set seed and create a random matrix of genotypes
set.seed(10)
genotypes <- matrix(rpois(50, 0.5), nrow = 10)

# simulate the number of reads with the reference allele
computeReference(genotypes = genotypes, indContribution = indContribution, error = 0.01)