| 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 |
| numberReferencePop | Compute the number of reference reads for multiple populations |
| Pfreqs | Compute allele frequencies from pooled sequencing 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 |
| simReads | Simulate coverage at a single locus |
| simulateCoverage | Simulate total number of reads per site |