API for acidgenomics/r-acidexperiment
Acid Genomics Summarized Experiment

Global functions
.centerSizeFactors	Source code
.exportAssays	Source code
.exportDF	Source code
.interconvertGenesAndSymbols	Source code
.isSampleData	Source code
.makeGeneMap	Source code
.mapGenes	Source code
AcidExperiment	Man page
AcidExperiment-package	Man page
AcidExperimentTestsUrl	Man page
EnsemblToNcbi	Man page
EnsemblToNcbi,RangedSummarizedExperiment-method	Man page
GeneToSymbol	Man page
GeneToSymbol,SummarizedExperiment-method	Man page
NcbiToEnsembl	Man page
TxToGene	Man page
TxToGene,SummarizedExperiment-method	Man page
aggregate	Man page
aggregate,Matrix-method	Man page
aggregate,SummarizedExperiment-method	Man page
aggregate,matrix-method	Man page
aggregateCols	Man page
aggregateCols,Matrix-method	Man page
aggregateCols,SummarizedExperiment-method	Man page
aggregateCols,matrix-method	Man page
aggregateRows	Man page
aggregateRows,Matrix-method	Man page
aggregateRows,SummarizedExperiment-method	Man page
aggregateRows,matrix-method	Man page
as.SummarizedExperiment	Man page
as.SummarizedExperiment,RangedSummarizedExperiment-method	Man page
as.SummarizedExperiment,SummarizedExperiment-method	Man page
autopadZeros	Man page
autopadZeros,SummarizedExperiment-method	Man page
autopadZeros,matrix-method	Man page
calculateMetrics	Man page
calculateMetrics,Matrix-method	Man page
calculateMetrics,SummarizedExperiment-method	Man page
calculateMetrics,matrix-method	Man page
camelCase	Man page
camelCase,DFrame-method	Man page
camelCase,Matrix-method	Man page
camelCase,Ranges-method	Man page
camelCase,SummarizedExperiment-method	Man page
camelCase,Vector-method	Man page
camelCase,atomic-method	Man page
camelCase,data.frame-method	Man page
camelCase,factor-method	Man page
camelCase,list-method	Man page
camelCase,matrix-method	Man page
combine	Man page
combine,SummarizedExperiment,SummarizedExperiment-method	Man page
convertGenesToSymbols	Man page
convertGenesToSymbols,SummarizedExperiment-method	Man page
convertSampleIdsToNames	Man page
convertSampleIdsToNames,SummarizedExperiment-method	Man page
convertSymbolsToGenes	Man page
convertSymbolsToGenes,SummarizedExperiment-method	Man page
convertTranscriptsToGenes	Man page
convertTranscriptsToGenes,Matrix-method	Man page
convertTranscriptsToGenes,SummarizedExperiment-method	Man page
convertTranscriptsToGenes,character-method	Man page
convertTranscriptsToGenes,matrix-method	Man page
correlation	Man page
correlation,Matrix,Matrix-method	Man page
correlation,Matrix,missingOrNULL-method	Man page
correlation,SummarizedExperiment,SummarizedExperiment-method	Man page
correlation,SummarizedExperiment,missingOrNULL-method	Man page
correlation,matrix,matrix-method	Man page
correlation,matrix,missingOrNULL-method	Man page
correlation,numeric,numeric-method	Man page
counts	Man page
counts,SummarizedExperiment-method	Man page
counts<-	Man page
counts<-,SummarizedExperiment,Matrix-method	Man page
counts<-,SummarizedExperiment,matrix-method	Man page
decode	Man page
decode,SummarizedExperiment-method	Man page
detectLanes	Man page Source code
dottedCase	Man page
dottedCase,DFrame-method	Man page
dottedCase,Matrix-method	Man page
dottedCase,Ranges-method	Man page
dottedCase,SummarizedExperiment-method	Man page
dottedCase,Vector-method	Man page
dottedCase,atomic-method	Man page
dottedCase,data.frame-method	Man page
dottedCase,factor-method	Man page
dottedCase,list-method	Man page
dottedCase,matrix-method	Man page
droplevels2	Man page
droplevels2,SummarizedExperiment-method	Man page
encode	Man page
encode,SummarizedExperiment-method	Man page
estimateSizeFactors	Man page
estimateSizeFactors,SummarizedExperiment-method	Man page
export	Man page
export,SummarizedExperiment,character-method	Man page
geneNames	Man page
geneNames,GRanges-method	Man page
geneNames,SummarizedExperiment-method	Man page
headtail	Man page
headtail,DFrame-method	Man page
headtail,GRanges-method	Man page
headtail,Matrix-method	Man page
headtail,SummarizedExperiment-method	Man page
humanize	Man page
humanize,SummarizedExperiment-method	Man page
importSampleData	Man page Source code
integerCounts	Man page
integerCounts,Matrix-method	Man page
integerCounts,SummarizedExperiment-method	Man page
integerCounts,matrix-method	Man page
interestingGroups	Man page
interestingGroups,Annotated-method	Man page
interestingGroups<-	Man page
interestingGroups<-,Annotated,NULL-method	Man page
interestingGroups<-,Annotated,character-method	Man page
interestingGroups<-,SummarizedExperiment,character-method	Man page
makeSampleData	Man page
makeSampleData,DFrame-method	Man page
makeSampleData,data.frame-method	Man page
makeSummarizedExperiment	Man page Source code
mapGenes	Man page
mapGenesToIds	Man page
mapGenesToIds,SummarizedExperiment-method	Man page
mapGenesToRownames	Man page
mapGenesToRownames,SummarizedExperiment-method	Man page
mapGenesToSymbols	Man page
mapGenesToSymbols,SummarizedExperiment-method	Man page
matchInterestingGroups	Man page Source code
matchSampleColumn	Man page
matchSampleColumn,DFrame-method	Man page
matchSampleColumn,SummarizedExperiment-method	Man page
melt	Man page
melt,Matrix-method	Man page
melt,SummarizedExperiment-method	Man page
metrics	Man page
metrics,SummarizedExperiment-method	Man page
microplate	Man page Source code
minimalSampleData	Man page Source code
nonzeroRowsAndCols	Man page
nonzeroRowsAndCols,Matrix-method	Man page
nonzeroRowsAndCols,SummarizedExperiment-method	Man page
nonzeroRowsAndCols,matrix-method	Man page
organism	Man page
organism,SummarizedExperiment-method	Man page
organism<-	Man page
sampleData	Man page
sampleData,SummarizedExperiment-method	Man page
sampleData<-	Man page
sampleData<-,SummarizedExperiment,DFrame-method	Man page
sampleNames	Man page
sampleNames,SummarizedExperiment-method	Man page
sampleNames<-	Man page
sampleNames<-,SummarizedExperiment,character-method	Man page
sanitizeSampleData	Man page Source code
selectSamples	Man page
selectSamples,SummarizedExperiment-method	Man page
sizeFactors	Man page
sizeFactors,SummarizedExperiment-method	Man page
sizeFactors<-	Man page
sizeFactors<-,SummarizedExperiment-method	Man page
snakeCase	Man page
snakeCase,DFrame-method	Man page
snakeCase,Matrix-method	Man page
snakeCase,Ranges-method	Man page
snakeCase,SummarizedExperiment-method	Man page
snakeCase,Vector-method	Man page
snakeCase,atomic-method	Man page
snakeCase,data.frame-method	Man page
snakeCase,factor-method	Man page
snakeCase,list-method	Man page
snakeCase,matrix-method	Man page
stripGeneVersions	Man page
stripGeneVersions,SummarizedExperiment-method	Man page
stripTranscriptVersions	Man page
stripTranscriptVersions,SummarizedExperiment-method	Man page
syntactic	Man page
tpm	Man page
tpm,SummarizedExperiment-method	Man page
uniteInterestingGroups	Man page
uniteInterestingGroups,DFrame-method	Man page
upperCamelCase	Man page
upperCamelCase,DFrame-method	Man page
upperCamelCase,Matrix-method	Man page
upperCamelCase,Ranges-method	Man page
upperCamelCase,SummarizedExperiment-method	Man page
upperCamelCase,Vector-method	Man page
upperCamelCase,atomic-method	Man page
upperCamelCase,data.frame-method	Man page
upperCamelCase,factor-method	Man page
upperCamelCase,list-method	Man page
upperCamelCase,matrix-method	Man page