indReads: Reads contributed by each individual

In poolHelper: Simulates Pooled Sequencing Genetic Data

Reads contributed by each individual

Description

This function simulates the contribution, in terms of reads, of each individual of a given pool. Please note that this function works for a single pool and should not be directly applied to situations where multiple pools were used.

Usage

indReads(np, coverage, probs)

Arguments

np	an integer specifying how many individuals were pooled.
coverage	a vector containing the total depth of coverage of a given pool. Each entry of the vector represents a different site.
probs	a matrix containing the probability of contribution of each individual. This matrix can be obtained with the indProbs function.

Value

a matrix with the number of reads contributed by each individual towards the coverage of its pool. Each row of the matrix is a different individual and each column a different site.

Examples

# probability of contribution for 10 individuals at 5 sites
probs <- indProbs(np = 10, nSNPs = 5, pError = 100)

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

poolHelper documentation built on July 9, 2023, 6:23 p.m.