Man pages for nuno-agostinho/cTRAP
Identification of candidate causal perturbations from differential gene expression data

analyseDrugSetEnrichmentAnalyse drug set enrichment
as.table.similarPerturbationsCross Tabulation and Table Creation
calculateCellLineMeanCalculate cell line mean
checkColnamesCheck whether 'test_names' are columns in the 'data.frame'
chunkVectorAssign vector elements into chunks
closeOpenHandlesClose open handles
cmapMetadataCMap metadata
cmapPerturbationsCompoundsCMap perturbations sample for small molecules
cmapPerturbationsKDCMap perturbations sample for knockdown experiments
compareAgainstReferenceCompare multiple methods and rank reference accordingly
compareAgainstReferencePerMethodCompare single method
compareQuantileCompare vector against its quantile
convertENSEMBLtoGeneSymbolsConvert ENSEMBL gene identifiers to gene symbols
correlateAgainstReferenceCorrelate against data columns
countsGene expression data sample
cTRAPcTRAP package
diffExprStatDifferential expression's t-statistics sample
dimnames.perturbationChangesDimnames of a 'perturbationChanges' object
dim.perturbationChangesDimensions of a 'perturbationChanges' object
downloadENCODEknockdownMetadataDownload metadata for ENCODE knockdown experiments
downloadIfNotFoundDownload data if given file is not found
ENCODEmetadataENCODE metadata sample
filterCMapMetadataFilter CMap metadata
fix.datatypesAdjust the data types for columns of a meta data frame
GCT-classAn S4 class to represent a GCT object
getCMapConditionsList available conditions in CMap datasets
getCMapPerturbationTypesGet perturbation types
getENCODEcontrolsGet experiments files for a given control
loadCMapDataLoad CMap data
loadCMapZscoresLoad matrix of CMap perturbation's differential expression...
loadCTRPgeneExpressionLoad CTRP data
loadDrugDescriptorsLoad table with drug descriptors
loadENCODEsampleLoad ENCODE sample
loadENCODEsamplesLoad ENCODE samples
loadExpressionDrugSensitivityAssociationLoad gene expression and drug sensitivity correlation matrix
loadNCI60drugSensitivityLoad CTRP data
matchStatsWithDrugSetsIDMatch identifiers between data and drug sets
parseCMapIDParse CMap identifier
performDifferentialExpressionPerform differential gene expression based on ENCODE data
performGSEAPerform GSEA
performGSEAagainstReferencePerform gene set enrichment (GSA) against data columns
plotDrugSetEnrichmentPlot drug set enrichment
plotESplotRender GSEA enrichment plot
plotGSEAPlot gene set enrichment analysis (GSEA)
plotMetricDistributionPlot metric distribution
plot.perturbationChangesPlot perturbation comparison against a differential...
plot.referenceComparisonPlot data comparison
plotSingleCorrRender scatter plot to show a single relationship
plotTargetingDrugsVSsimilarPerturbationsPlot similar perturbations against predicted targeting drugs
predictTargetingDrugsPredict targeting drugs
prepareCMapPerturbationsPrepare CMap perturbation data
prepareDrugSetsPrepare drug sets from a table with compound descriptors
prepareENCODEgeneExpressionLoad an ENCODE gene expression data
prepareExpressionDrugSensitivityAssociationPrepare gene expression and drug sensitivity correlation...
prepareGSEApathwaysPrepare GSEA pathways
print.similarPerturbationsPrint a 'similarPerturbations' object
processByChunksProcess data column by chunks
processIdsReturn a subset of requested GCTX row/colum ids out of the...
rankColumnsRank columns in a dataset
rankSimilarPerturbationsRank CMap perturbations' similarity to a differential...
readGctxIdsRead GCTX row or column ids
readGctxMetaParse row or column metadata from GCTX files
stripStrStrip non-alpha-numeric characters from a string
sub-.perturbationChangesSubset a 'perturbationChanges' object
subsetToIdsDo a robust 'data.frame' subset to a set of ids
nuno-agostinho/cTRAP documentation built on Nov. 13, 2019, 3:31 p.m.