| alleleCounts | Return allele counts from a genofile based on read counts |
| bafMatrix | Compute B-allele frequency spectrum genome-wide |
| barcodes | Generate GenomicRanges object from GDS file |
| binommix | Fit binomial mixture model on coverage data |
| binommixCDF | CDF for binomial mixture model |
| callMajor | Get major allele calls for isolates from BAF matrix |
| ciMM | Generate Confidence Intervals for parameter estimates using... |
| coverageBySample | SNP coverage rates by sample thresholds |
| coverageBySNP | Sample coverage rates by SNP thresholds |
| dtbeta | Truncated beta distribution |
| dtexp | Truncated exponential distrubition |
| extractBarcode | Extract barcode for use in COIL program |
| extractPED | Extract PED files from gds |
| gambian_isolates | Plasmodium falciparum SNV data from Gambia. |
| generateWindows | Construct non-overlapping Genomic Windows by Chromosome |
| getBarcodeVariants | Helper functions for extracting variant IDs corresponding to... |
| getCoordinates | Helper function for producing data frame of genomic... |
| getDosage | Helper function for producing matrix of allele dosages |
| getFws | Compute Fws within-host diversity statistic |
| getGATKInfo | Get GATK info tags |
| getHeterozygosity | Compute population level heterozygosity |
| getHeterozygosityBySample | Compute heterozygosity by sample |
| getMAF | Compute minor allele frequency |
| getMSE | Model assessment for fitted model using MSE |
| getTheta | Return estimated model parameters |
| infomat | Fisher Information Approximation |
| maf_summary | Minor Allele Frequenies of ~ 30,000 Plasmodium falciparum... |
| moimix | Evaluate muliplicity of infection in malaria parasites |
| mse | Mean Square Error for binomial mixture model |
| perSiteAlleleCoverage | Compute per site per sample coverage |
| perSiteCoverage | Compute per variant depth accross all samples. |
| perSiteCoverageBySample | Compute the proportion of samples covered up any number of... |
| perSiteCoverageBySNP | Compute proportion of SNPs covered up to a lower bound of... |
| plot.bafMatrix | Plot bafMatrix object |
| readEstMOI | Parse estMOI log files in a directory into tidy data frame |
| rtexp | Truncated exponential distribution random number generation |
| sampleMM | Generate iid binomial mixture random variables for testing EM... |
| scaledProportion | sum number of samples/snps meeting coverage threshold scaled... |
| seMM | Compute standard errors for mixture model parameter estimates |
| simulateMOI | Simple simulation of MOI SNV data |
