Simulates Pooled Sequencing Genetic Data

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Documentation for package ‘poolHelper’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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