removeSites {poolHelper}

Apply a minor allele reads threshold

Description

Removes sites where the total number of minor-allele reads is below a certain threshold.

Usage

removeSites(freqs, alternative, coverage, minor, min.minor)

Arguments

freqs

a vector of allele frequencies where each entry corresponds to a different site.

alternative

a matrix with the number of reads with the alternative allele. 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.

minor

a matrix with the number of minor-allele reads. 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.

Details

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 three named entries:

freqs

is a vector with the allele frequencies minus the frequency of the removed sites.

alternative

is a matrix with the number of alternative-allele reads per site, minus any removed sites.

coverage

is a matrix with the depth of coverage minus the coverage of the removed sites.

Examples

# 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

# find the minor allele at each site
minor <- findMinor(reference = reference, alternative = alternative, coverage = coverage)
# keep only the matrix with the minor allele reads
minor <- minor[["minor"]]

# remove sites where the number of minor-allele reads is below the threshold
removeSites(freqs = freqs, alternative = alternative, coverage = coverage,
minor = minor, min.minor = 2)