poolHelper (version 1.1.0)

popsReads: Simulate total number of reads for multiple populations

Description

Simulates the contribution of each individual towards the total coverage of its population.

Usage

popsReads(list_np, coverage, pError)

Value

a list with one entry per population. Each entry represents the number of reads contributed by each individual towards the total coverage of its population. Different individuals correspond to different rows and different sites to different columns.

Arguments

list_np

is a list where each entry corresponds to a different population. Each entry is a vector and each vector 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 matrix containing the total depth of coverage of all populations. Each row corresponds to a different population and each column to 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. These steps will be performed for each population, thus obtaining the number of reads contributed by each individual for each population.

Examples

# simulate coverage for two populations sequenced at 10x at 5 sites
reads <- simulateCoverage(mean = c(10, 10), variance = c(20, 20), nSNPs = 5, nLoci = 1)

# simulate the individual contribution towards that coverage
# assuming that the first population was sequenced using two pools of 5 individuals
# and the second using a single pool with 10 individuals
popsReads(list_np = list(c(5, 5), 10), coverage = reads, pError = 5)