poolHelper (version 1.1.0)

popReads: Compute number of reads for each individual and across all sites

Description

This function computes the contribution of each individual towards the total coverage of a given population.

Usage

popReads(vector_np, coverage, pError)

Value

a matrix with the number of reads contributed by each individual. Each row of the matrix corresponds to a different individual and each column to a different site.

Arguments

vector_np

is a vector where each entry contains the number of diploid individuals of a given pool. Thus, if a population was sequenced using two pools, each with 10 individuals, this vector would contain two entries and both will be 10.

coverage

a vector containing the total depth of coverage of the population. Each entry of the vector represents a different site.

pError

an integer representing the value of the error associated with DNA pooling. This value is related with the unequal contribution of both individuals and pools towards the total number of reads observed for a given population - the higher the value the more unequal are the individual and pool contributions.

Details

If multiple pools were used to sequence a population, this will compute the contribution of each pool and then use that to calculate how many reads does that pool contribute. Next, the probability of contribution of each individual is computed and utilized to calculate the number of reads that each individual contributes towards the total number of reads observed in the corresponding pool.

Examples

# simulate number of reads contributed by each individual towards the total population coverage
# assuming a coverage of 10x at 5 sites and two pools, each with 5 individuals
popReads(vector_np = c(5, 5), coverage = rep(10, 5), pError = 100)