Man pages for bahlolab/moimix
Estimating mulitplicity of infection from high-throughput sequencing data

alleleCountsReturn allele counts from a genofile based on read counts
bafMatrixCompute B-allele frequency spectrum genome-wide
barcodesGenerate GenomicRanges object from GDS file
binommixFit binomial mixture model on coverage data
binommixCDFCDF for binomial mixture model
callMajorGet major allele calls for isolates from BAF matrix
ciMMGenerate Confidence Intervals for parameter estimates using...
collapseProbsCollapse allele frequency to half axis
coverageBySampleSNP coverage rates by sample thresholds
coverageBySNPSample coverage rates by SNP thresholds
dtbetaTruncated beta distribution
dtexpTruncated exponential distrubition
extractBarcodeExtract barcode for use in COIL program
extractPEDExtract PED files from gds
gambian_isolatesPlasmodium falciparum SNV data from Gambia.
generateWindowsConstruct non-overlapping Genomic Windows by Chromosome
getBarcodeVariantsHelper functions for extracting variant IDs corresponding to...
getCoordinatesHelper function for producing data frame of genomic...
getDosageHelper function for producing matrix of allele dosages
getFwsCompute Fws within-host diversity statistic
getGATKInfoGet GATK info tags
getHeterozygosityCompute population level heterozygosity
getHeterozygosityBySampleCompute heterozygosity by sample
getMAFCompute minor allele frequency
getMSEModel assessment for fitted model using MSE
getThetaReturn estimated model parameters
global_pfalciparum_snpsMinor Allele Frequenies of ~ 86,000 Plasmodium falciparum...
infomatFisher Information Approximation
moimixEvaluate muliplicity of infection in malaria parasites
mseMean Square Error for binomial mixture model
perSiteAlleleCoverageCompute per site per sample coverage
perSiteCoverageCompute per variant depth accross all samples.
perSiteCoverageBySampleCompute the proportion of samples covered up any number of...
perSiteCoverageBySNPCompute proportion of SNPs covered up to a lower bound of...
plot.bafMatrixPlot bafMatrix object
processGATKProcess GATK files
processVarscanProcess varscan files
qtbeta@describeIn dtbeta Quantile function @param p vector of...
readEstMOIParse estMOI log files in a directory into tidy data frame
rtexpTruncated exponential distribution random number generation
sampleMMGenerate iid binomial mixture random variables for testing EM...
scaledProportionsum number of samples/snps meeting coverage threshold scaled...
seMMCompute standard errors for mixture model parameter estimates
simulateMOISimple simulation of MOI SNV data
toProbConvert odds to probability
bahlolab/moimix documentation built on May 17, 2018, 10:34 p.m.