API for ramwas
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
| 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 |
