Pfreqs {poolHelper}

Compute allele frequencies from pooled sequencing data

Description

Computes the frequency of the alternative allele in Pool-seq data and removes any site with too few minor-allele reads from both the pool frequencies and the frequencies computed directly from genotypes.

Usage

Pfreqs(reference, alternative, coverage, min.minor, ifreqs)

Arguments

reference

a matrix with the number of reference allele reads. Each row should be a different population and each column a different site.

alternative

a matrix with the number of alternative allele reads. Each row should be a different population and each column a different site.

coverage

a matrix with the total coverage. Each row should be a different population and each column a different site.

min.minor

is an integer representing the minimum allowed number of minor-allele reads. Sites that, across all populations, have less minor-allele reads than this threshold will be removed from the data.

ifreqs

a vector of allele frequencies computed directly from the genotypes where each entry corresponds to a different site.

Details

The frequency at a given SNP is calculated according to: pi = c/r, where c = number of alternative allele reads and r = total number of observed reads. Additionally, if a site has less minor-allele reads than min.minor across all populations, that site is removed from the data.

Value

a list with two entries. The ifreqs entry contains the allele frequencies computed directly from genotypes and pfreqs the allele frequencies computed from pooled sequencing data.

Examples

set.seed(10)
# create a vector of allele frequencies
freqs <- runif(20)
set.seed(10)
# create a matrix with the number of reads with the alternative allele
alternative <- matrix(sample(x = c(0,5,10), size = 20, replace = TRUE), nrow = 1)
# create a matrix with the depth of coverage
coverage <- matrix(sample(100:150, size = 20), nrow = 1)
# the number of reads with the reference allele is obtained by subtracting
# the number of alternative allele reads from the depth of coverage
reference <- coverage - alternative
# compute allele frequencies from pooled sequencing data
Pfreqs(reference = reference, alternative = alternative, coverage = coverage,
min.minor = 2, ifreqs = freqs)