R: Simulates Pooled Sequencing Genetic Data

# Simulates Pooled Sequencing Genetic Data

## Documentation for package ‘poolHelper’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculatePi | Calculate population frequency at each SNP
computeReference | Compute the number of reference reads over a matrix
errorHet | Average absolute difference between expected heterozygosity
findMinor | Define major and minor alleles
getNumReadsR_vector | Compute the number of reference reads
Ifreqs | Compute allele frequencies from genotypes
indProbs | Probability of contribution of each individual
indReads | Reads contributed by each individual
maeFreqs | Average absolute difference between allele frequencies computed from genotypes and from Pool-seq data
maeHet | Average absolute difference between the expected heterozygosity computed from genotypes and from Pool-seq data
maePool | Average absolute difference between allele frequencies
mymae | Average absolute difference between allele frequencies computed from genotypes supplied by the user and from Pool-seq data
numberReferencePop | Compute the number of reference reads for multiple populations
Pfreqs | Compute allele frequencies from pooled sequencing data
pool2sync | Create 'synchronized' file from Pool-seq data
pool2vcf | Create VCF file from Pool-seq data
poolPops | Create Pooled DNA sequencing data for multiple populations
poolProbs | Probability of contribution of each pool
poolReads | Reads contributed by each pool
popReads | Compute number of reads for each individual and across all sites
popsReads | Simulate total number of reads for multiple populations
removeSites | Apply a minor allele reads threshold
remove_by_reads | Apply a coverage-based filter over a list
remove_by_reads_matrix | Apply a coverage-based filter to a matrix
run_scrm | Simulate a single population
simPoolseq | Simulate Pool-seq data
simReads | Simulate coverage at a single locus
simulateCoverage | Simulate total number of reads per site