Global functions | |
---|---|
.calc.coverage.chr | Source code |
.combine.bams.qc | Source code |
.count.nonCpG.reads.forward | Source code |
.count.nonCpG.reads.reverse | Source code |
.dump | Source code |
.file.remove | Source code |
.getCovariates | Source code |
.hist.isodist.forward | Source code |
.hist.isodist.reverse | Source code |
.histmean | Source code |
.log | Source code |
.logErrors | Source code |
.matchCovmatCovar | Source code |
.my.hist.plot | Source code |
.notnull | Source code |
.qcTextLineR | Source code |
.qcTextLineT | Source code |
.ramwas0cadJob | Source code |
.ramwas1scanBamJob | Source code |
.ramwas3coverageJob | Source code |
.ramwas3normalizeJob | Source code |
.ramwas3transposeFilterJob | Source code |
.ramwas4PCAjob | Source code |
.ramwas5MWASjob | Source code |
.ramwasSNPsJob | Source code |
.showErrors | Source code |
.testCovariates | Source code |
`%add%` | Source code |
bam.chrXY.qc | Source code |
bam.count.nonCpG.reads | Source code |
bam.coverage.by.density | Source code |
bam.hist.isolated.distances | Source code |
bam.removeRepeats | Source code |
bam.scanBamFile | Source code |
cachedRDSload | Man page Source code |
calc.coverage | Source code |
colSumsSq | Man page Source code |
combineBamQcIntoSamples | Source code |
estimateCellTypes | Source code |
estimateFragmentSizeDistribution | Man page Source code |
findBestNpvs | Man page Source code |
getCpGsetALL | Man page Source code |
getCpGsetCG | Man page Source code |
getDataByLocation | Man page Source code |
getLocations | Man page Source code |
getMWAS | Man page Source code |
getMWASandLocations | Man page Source code |
getMWASrange | Man page Source code |
groupSample | Source code |
injectSNPsMAF | Man page Source code |
insilicoFASTQ | Man page Source code |
isAbsolutePath | Man page Source code |
isocpgSitesFromCpGset | Source code |
loadBamQC | Source code |
madeBED | Man page Source code |
madeBEDgraph | Man page Source code |
madeBEDgraphRange | Man page Source code |
madeBEDrange | Man page Source code |
makefullpath | Man page Source code |
manPlotFast | Man page |
manPlotPrepare | Man page |
mat2cols | Man page Source code |
noncpgSitesFromCpGset | Source code |
orthonormalizeCovariates | Man page Source code |
parameterDump | Man page Source code |
parameterPreprocess | Man page Source code |
parametersFromFile | Man page Source code |
parseBam2sample | Source code |
pipeline | Man page |
pipelineCoverage1Sample | Source code |
pipelineProcessBam | Man page Source code |
pipelineSaveQCplots | Source code |
plot.qcCoverageByDensity | Man page Source code |
plot.qcEditDist | Man page Source code |
plot.qcEditDistBF | Man page Source code |
plot.qcHistScore | Man page Source code |
plot.qcHistScoreBF | Man page Source code |
plot.qcIsoDist | Man page Source code |
plot.qcLengthMatched | Man page Source code |
plot.qcLengthMatchedBF | Man page Source code |
plotCVcors | Man page Source code |
plotFragmentSizeDistributionEstimate | Man page Source code |
plotPCvalues | Man page Source code |
plotPCvectors | Man page Source code |
plotPrediction | Man page Source code |
plotROC | Man page Source code |
postPCAprocessing | Source code |
predictionStats | Source code |
processCommandLine | Man page Source code |
pvalue2qvalue | Man page Source code |
qcmean | Man page Source code |
qcmean.NULL | Man page Source code |
qcmean.qcChrX | Man page Source code |
qcmean.qcChrY | Man page Source code |
qcmean.qcCoverageByDensity | Man page Source code |
qcmean.qcEditDist | Man page Source code |
qcmean.qcEditDistBF | Man page Source code |
qcmean.qcFrwrev | Man page Source code |
qcmean.qcHistScore | Man page Source code |
qcmean.qcHistScoreBF | Man page Source code |
qcmean.qcIsoDist | Man page Source code |
qcmean.qcLengthMatched | Man page Source code |
qcmean.qcLengthMatchedBF | Man page Source code |
qcmean.qcNonCpGreads | Man page Source code |
qqPlotFast | Man page Source code |
qqPlotPrepare | Man page Source code |
ramwas | Man page |
ramwas-package | Man page |
ramwas0createArtificialData | Man page Source code |
ramwas1scanBams | Man page Source code |
ramwas2collectqc | Man page Source code |
ramwas3normalizedCoverage | Man page Source code |
ramwas4PCA | Man page Source code |
ramwas5MWAS | Man page Source code |
ramwas5saveTopFindings | Source code |
ramwas5saveTopFindingsSNPs | Source code |
ramwas6annotateTopFindings | Man page Source code |
ramwas7ArunMWASes | Man page Source code |
ramwas7BrunElasticNet | Man page Source code |
ramwas7CplotByNCpGs | Man page Source code |
ramwas7riskScoreCV | Man page Source code |
ramwasAnnotateLocations | Man page Source code |
ramwasPCsCovariateSelection | Source code |
ramwasParameters | Man page Source code |
ramwasSNPs | Man page Source code |
remove.repeats.over.maxrep | Source code |
rowSumsSq | Man page Source code |
rwDataClass | Man page |
rwDataClass-class | Man page |
subsetCoverageDirByLocation | Man page Source code |
testPhenotype | Man page Source code |
trimBamFilename | Source code |
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