remove_quantileReads {poolABC}

Remove sites using quantiles of the depth of coverage

Description

Removes sites that have too many or too few reads from the dataset.

Usage

remove_quantileReads(nPops, data)

Arguments

nPops

is an integer representing the total number of populations in the dataset.

data

is a dataset containing information about real populations. This dataset should have lists with the allelic frequencies, the position of the SNPs, the range of the contig, the number of major allele reads, the number of minor allele reads and the depth of coverage.

Details

The 25% and the 75% quantiles of the coverage distribution is computed for each population in the dataset. Then, the lowest 25% quantile across all populations is considered the minimum depth of coverage allowed. Similarly, the highest 75% quantile across all populations is considered the maximum depth of coverage allowed. The coverage of each population at each site is compared with those threshold values and any site, where the coverage of at least one population is below or above that threshold, is completely removed from the dataset.

Value

a list with the following elements:

freqs

a list with the allele frequencies, computed by dividing the number of minor-allele reads by the total coverage. Each entry of this list corresponds to a different contig. Each entry is a matrix where each row is a different site and each column is a different population.

positions

a list with the positions of each SNP. Each entry of this list is a vector corresponding to a different contig.

range

a list with the minimum and maximum SNP position of each contig. Each entry of this list is a vector corresponding to a different contig.

rMajor

a list with the number of major-allele reads. Each entry of this list corresponds to a different contig. Each entry is a matrix where each row is a different site and each column is a different population.

rMinor

a list with the number of minor-allele reads. Each entry of this list corresponds to a different contig. Each entry is a matrix where each row is a different site and each column is a different population.

coverage

a list with the total coverage. Each entry of this list corresponds to a different contig. Each entry is a matrix where each row is a different site and each column is a different population.

This output is identical to the data input, the only difference being the removal of sites with too many or too few reads.

Examples

# load the data from one rc file
data(rc1)

# clean and organize the data in this single file
mydata <- cleanData(file = rc1, pops = 7:10)

# organize the information by contigs
mydata <- prepareFile(data = mydata, nPops = 4)

# remove sites according to the coverage quantile
remove_quantileReads(nPops = 4, data = mydata)