Man pages for cTRAP
Identification of candidate causal perturbations from differential gene expression data
| analyseDrugSetEnrichment | Analyse drug set enrichment |
| as.table.referenceComparison | Cross Tabulation and Table Creation |
| calculateCellLineMean | Calculate cell line mean |
| checkColnames | Check whether 'test_names' are columns in the 'data.frame' |
| chunkVector | Assign vector elements into chunks |
| closeOpenHandles | Close open handles |
| cmapMetadata | CMap metadata |
| cmapPerturbationsCompounds | CMap perturbations sample for small molecules |
| cmapPerturbationsKD | CMap perturbations sample for knockdown experiments |
| compareAgainstReference | Compare multiple methods and rank reference accordingly |
| compareAgainstReferencePerMethod | Compare single method |
| compareQuantile | Compare vector against its quantile |
| convertENSEMBLtoGeneSymbols | Convert ENSEMBL gene identifiers to gene symbols |
| correlateAgainstReference | Correlate against data columns |
| counts | Gene expression data sample |
| cTRAP | cTRAP package |
| diffExprStat | Differential expression's t-statistics sample |
| dot-plotBubbles | Plot packed bubbles |
| dot-prepareNavPage | Prepare Shiny page template |
| downloadENCODEknockdownMetadata | Download metadata for ENCODE knockdown experiments |
| downloadIfNotFound | Download data if given file is not found |
| ENCODEmetadata | ENCODE metadata sample |
| filterCMapMetadata | Filter CMap metadata |
| findIntersectingCompounds | Check for intersecting compounds across specific columns on... |
| fix.datatypes | Adjust the data types for columns of a meta data frame |
| GCT-class | An S4 class to represent a GCT object |
| getCMapConditions | List available conditions in CMap datasets |
| getCMapPerturbationTypes | Get CMap perturbation types |
| getENCODEcontrols | Get experiments files for a given control |
| launchCMapDataLoader | Load CMap data via a visual interface |
| launchDiffExprLoader | Load differential expression data via a visual interface |
| launchMetadataViewer | View metadata via a visual interface |
| launchResultPlotter | View and plot results via a visual interface |
| listExpressionDrugSensitivityAssociation | List available gene expression and drug sensitivity... |
| loadCMapData | Load CMap data |
| loadCMapZscores | Load matrix of CMap perturbation's differential expression... |
| loadCTRPgeneExpression | Load CTRP data |
| loadDrugDescriptors | Load table with drug descriptors |
| loadENCODEsample | Load ENCODE sample |
| loadENCODEsamples | Load ENCODE samples |
| loadExpressionDrugSensitivityAssociation | Load gene expression and drug sensitivity correlation matrix |
| loadNCI60drugSensitivity | Load CTRP data |
| matchStatsWithDrugSetsID | Match identifiers between data and drug sets |
| parseCMapID | Parse CMap identifier |
| performDifferentialExpression | Perform differential gene expression based on ENCODE data |
| performGSEA | Perform GSEA |
| performGSEAagainstReference | Perform gene set enrichment (GSA) against data columns |
| plotDrugSetEnrichment | Plot drug set enrichment |
| plotESplot | Render GSEA enrichment plot |
| plotGSEA | Plot gene set enrichment analysis (GSEA) |
| plotMetricDistribution | Plot metric distribution |
| plot.perturbationChanges | Operations on a 'perturbationChanges' object |
| plot.referenceComparison | Plot data comparison |
| plotSingleCorr | Render scatter plot to show a single relationship |
| plotTargetingDrugsVSsimilarPerturbations | Plot similar perturbations against predicted targeting drugs |
| predictTargetingDrugs | Predict targeting drugs |
| prepareCMapPerturbations | Prepare CMap perturbation data |
| prepareDrugSets | Prepare drug sets from a table with compound descriptors |
| prepareENCODEgeneExpression | Load ENCODE gene expression data |
| prepareExpressionDrugSensitivityAssociation | Prepare gene expression and drug sensitivity correlation... |
| prepareGSEAgenesets | Prepare GSEA gene sets |
| print.similarPerturbations | Print a 'similarPerturbations' object |
| processByChunks | Process data column by chunks |
| processIds | Return a subset of requested GCTX row/column ids out of the... |
| rankColumns | Rank columns in a dataset |
| rankSimilarPerturbations | Rank CMap perturbations' similarity to a differential... |
| readGctxIds | Read GCTX row or column ids |
| readGctxMeta | Parse row or column metadata from GCTX files |
| stripStr | Strip non-alpha-numeric characters from a string |
| subsetToIds | Do a robust 'data.frame' subset to a set of ids |
