poolHelper (version 1.1.0)

getNumReadsR_vector: Compute the number of reference reads

Description

This function takes as input the total depth of coverage and computes how many of those reads are reference allele reads.

Usage

getNumReadsR_vector(genotype_v, readCount_v, error)

Value

a vector with the number of reference allele reads. Each entry of the vector corresponds to a different individual.

Arguments

genotype_v

is a vector with the genotype of a given individual. Each entry of the vector should be a different site. Genotypes should be encoded as 0: reference homozygote, 1: heterozygote and 2: alternative homozygote.

readCount_v

is a vector with the number of reads contributed by the same given individual. Each entry of that vector should be a different 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.

Details

More precisely, this function computes the number of reference reads per site for one individual, given the genotype of the individual at each site, the total number of reads observed for the individual at that site and an error rate.

Examples

# number of reference allele reads for three individuals, each with 10x coverage
# one individual is homozygote for the reference allele (0), other is heterozygote (1)
# and the last is homozygote for the alternative allele (2)
getNumReadsR_vector(genotype_v = c(0,1,2), readCount_v = c(10, 10, 10), error = 0.01)