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poolHelper

Simulates Pooled Sequencing Genetic Data

This is the source code for the poolHelper R package. The main goal of this package is to provide tools to help researchers design their pooled sequencing studies.

The package provides functions to simulate pooled sequencing (Pool-seq) data under a variety of conditions. Users can define the average coverage, the number of individuals in the pool, the number of pools used and the Pool-seq error. The poolHelper package simulates the allele frequencies obtained with Pool-seq under different combinations of those parameters. These allele frequencies are then compared with the allele frequencies computed directly from the genotypes in the sample and the average absolute difference between both sets of allele frequencies is calculated.

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Install

install.packages('poolHelper')

Monthly Downloads

191

Version

1.1.0

License

GPL (>= 3)

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Repository

https://github.com/joao-mcarvalho/poolHelper

Maintainer

João Carvalho

Last Published

June 29th, 2023

Functions in poolHelper (1.1.0)

Create sync string for a single SNP

Randomly select the required number of loci from the pooled sequencing data

Calculate population frequency at each SNP

Filter Pool-seq data according to a minor-allele reads threshold

Filter sites according to a minor-allele reads threshold

Create 'synchronized' file from Pool-seq data

numberReferencePop

Compute the number of reference reads for multiple populations

Define major and minor alleles

Create genotypes from a output with haplotypes

Create VCF file from Pool-seq data

Compute number of reads for each individual and across all sites

Compute allele frequencies from genotypes

Probability of contribution of each individual

Average absolute difference between allele frequencies

Probability of contribution of each pool

Create Pooled DNA sequencing data for multiple populations

Simulate Pool-seq data

Convert haplotypes to genotypes

getNumReadsR_vector

Compute the number of reference reads

Simulate total number of reads for multiple populations

Average absolute difference between the expected heterozygosity computed from genotypes and from Pool-seq data

Create vcf string for all SNPs in a single locus

Average absolute difference between allele frequencies computed from genotypes supplied by the user and from Pool-seq data

Apply a minor allele reads threshold

Create vcf table with relevant information

remove_by_reads

Apply a coverage-based filter over a list

simulateCoverage

Simulate total number of reads per site

remove_by_reads_matrix

Apply a coverage-based filter to a matrix

Simulate coverage at a single locus

numberReference

Compute the number of reference reads at multiple loci

Create vcf string for a single SNP

Split matrix of genotypes

Simulate a single population

Reads contributed by each pool

Create vcf string for all SNPs in multiple loci

Compute expected heterozygosity per site

computeReference

Compute the number of reference reads over a matrix

Compute allele frequencies from pooled sequencing data

Compute expected heterozygosity within a population

Create invariable sites

Average absolute difference between expected heterozygosity

Average absolute difference between allele frequencies computed from genotypes and from Pool-seq data

Reads contributed by each individual