poolHelper (version 1.1.0)

simReads: Simulate coverage at a single locus

Description

Simulates the total number of reads, for each polymorphic site of a given locus using a negative binomial distribution.

Usage

simReads(mean, variance, nSNPs = NA, genotypes = NA)

Value

a matrix with the total coverage per population and per site. Different rows represent different populations and each column is a different site.

Arguments

mean

an integer that defines the mean depth of coverage to simulate. Please note that this represents the mean coverage across all sites. If a vector is supplied instead, the function assumes that each entry of the vector is the mean for a different population.

variance

an integer that defines the variance of the depth of coverage across all sites. If a vector is supplied instead, the function assumes that each entry of the vector is the variance for a different population.

nSNPs

an integer representing the number of polymorphic sites per locus to simulate. This is an optional input but either this or the genotypes matrix must be supplied.

genotypes

a matrix of simulated genotypes, where each column is a different SNP and each row is a different individual. This is an optional input but either this or the nSNPs must be supplied.

Details

The total number of reads is simulated with a negative binomial and according to a user-defined mean depth of coverage and variance. This function is intended to work with a matrix of genotypes, simulating the depth of coverage for each site present in the genotypes. However, it can also be used to simulate coverage distributions independent of genotypes, by choosing how many sites should be simulated (with the nSNPs option).

Examples

# coverage for one population at 10 sites
simReads(mean = 20, variance = 100, nSNPs = 10)

# simulate coverage at one locus with 10 SNPs for two populations:
# the first with 100x and the second with 50x
simReads(mean = c(100, 50), variance = c(250, 150), nSNPs = 10)