Man pages for quevedor2/CCLid
Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets
| addSegDat | addSegDat |
| affy.omni | Mapping of Omni 2.5M probesets to Affy SNP6.0 |
| annoDemoMat | annoDemoMat |
| annotateSegments | cnTools: annotate GRanges segments |
| assemblePredDat | assemblePredDat |
| assignGrpIDs | pIDs |
| availableRefCCL | availableRefCCL |
| bafDrift | bafDrift |
| balanceGrps | balanceGrps |
| ccl_table | Table containing links to external datasets and BAF matrices |
| checkAgainst | checkAgainst |
| checkForConcordance | checkForConcordance |
| checkMse | checkMse |
| cin70 | Chromosomal instability (CIN) 70 genes from... |
| combineSamples | combineSamples |
| compareVcf | compareVcf |
| corWithDrug | corWithDrug |
| demoSample | demoSample |
| dot-addCumPos | .addCumPos |
| dot-addSegSd | addSegSd |
| dot-blankGr | .blankGr |
| dot-chkAndDownload | Check and download |
| dot-compSegs | .compSegs |
| dot-demo | Demo |
| dot-demoDeconvolution | Title |
| dot-estimateDrift | .estimateDrift |
| dot-estimateZcutoff | .estimateZcutoff |
| dot-filt | .filt |
| dot-fixGT | .fixGT |
| dot-genMatchSnpDiff | .genMatchSnpDiff |
| dot-genNonmatchSnpDiff | .genNonmatchSnpDiff |
| dot-getChrLength | .getChrLength |
| dot-getDerivedFrom | .getDerivedFrom |
| dot-getDrift | .getDrift |
| dot-getSynonymous | .getSynonymous |
| dot-getVariantFeatures | .getVariantFeatures |
| dot-grepNA | .grepNA |
| dot-jsonToGr | .jsonToGr |
| dot-meltDf | Melts dataframe |
| dot-normBAF | .normBAF |
| dot-overlapProbeset | .overlapProbeset |
| dot-revComp | .revComp |
| dot-vcf2AffyGT | .vcf2AffyGT |
| dot-zval | z-statistic |
| downloadRefCCL | downloadRefCCL |
| driftOverlap | driftOverlap |
| driftOverlapMetric | driftOverlapMetric |
| findCclPairs | findCclPairs |
| formatRefMat | formatRefMat |
| fullpull | fullpull |
| genDemoData | genDemoData |
| genErrBp | genErrBp |
| getBafDrifts | getBafDrifts |
| getCinScore | getCinScore |
| getCNDrifts | getCnDrifts |
| getCVCL | getCVCL |
| getGeneExpr | getGeneExpr |
| getGenes | cnTools: get Genes in TxDb.Hsapiens.UCSC.hg19.knownGene |
| getSegSD | get Seg SD |
| getVcfDrifts | getVcfDrifts |
| gne.meta | Metadata for gCSI dataset |
| loadInPSets | loadInPSets |
| loadRef | loadRef |
| mapVariantFeat | mapVariantFeat |
| mapVcf2Affy | mapVcf2Affy |
| meta.df | Metadata mapping together all pharmacogenomic datasets and... |
| mkPredictions | mkPredictions |
| multiDriftPlot | multiDriftPlot OUTDATED |
| overlapPos | overlapPos |
| plot.CCLid | plot.CCLid plot() function for CCLid adjusted DNAcopy segment... |
| plotFracDrift | plotFracDrift |
| plotHist | plotHist |
| plot.multiObj | plot.multiObj |
| plot.SimpleCCLid | plot.SimpleCCLid |
| readinRnaFileMapping | readinRnaFileMapping |
| rna.meta.df | Metadata mapping together all pharmacogenomic datasets and... |
| segmentDrift | segmentDrift |
| sigDiffBaf | sigDiffBaf |
| similarityMatrix | similarityMatrix |
| snp6.dat | BED file of SNP6 Probeset IDs and genomic loci in hg19 |
| splitConcordanceVals | splitConcordanceVals |
| splitToMNM | splitToMNM |
| summarizeFracDrift | summarizeFracDrift |
| trainLogit | trainLogit |
