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 |
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