Acid Genomics Summarized Experiment

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Documentation for package ‘AcidExperiment’ version 0.2.2

• DESCRIPTION file.

Help Pages

A C D E G H I M N O S T U

-- A --

aggregate	Aggregate
aggregate-method	Aggregate
aggregateCols	Aggregate
aggregateCols-method	Aggregate
aggregateRows	Aggregate
aggregateRows-method	Aggregate
as.SummarizedExperiment	Coercion methods
as.SummarizedExperiment-method	Coercion methods
autopadZeros	Autopad zeros
autopadZeros-method	Autopad zeros

-- C --

calculateMetrics	Calculate quality control metrics
calculateMetrics-method	Calculate quality control metrics
camelCase	Syntactic naming functions
camelCase-method	Syntactic naming functions
coerce	Coercion methods
combine	Combine multiple objects
combine-method	Combine multiple objects
convertGenesToSymbols	Convert genes to symbols
convertGenesToSymbols-method	Convert genes to symbols
convertSampleIDsToNames	Convert sample identifiers to names
convertSampleIDsToNames-method	Convert sample identifiers to names
convertSymbolsToGenes	Convert genes to symbols
convertSymbolsToGenes-method	Convert genes to symbols
convertTranscriptsToGenes	Convert transcripts to genes
convertTranscriptsToGenes-method	Convert transcripts to genes
correlation	Correlation
correlation-method	Correlation
counts	Counts
counts-method	Counts
counts<-	Counts
counts<--method	Counts

-- D --

decode	Decode column data that uses run-length encoding
decode-method	Decode column data that uses run-length encoding
detectLanes	Detect sequencing lanes
dottedCase	Syntactic naming functions
dottedCase-method	Syntactic naming functions
droplevels	Drop unused levels from factors
droplevels-method	Drop unused levels from factors

-- E --

encode	Encode using run-length encoding
encode-method	Encode using run-length encoding
Ensembl2Entrez	Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-method	Ensembl-to-Entrez gene identifier mappings
Entrez2Ensembl	Ensembl-to-Entrez gene identifier mappings
estimateSizeFactors	Estimate size factors
estimateSizeFactors-method	Estimate size factors
export	Export
export-method	Export

-- G --

Gene2Symbol	Gene-to-symbol mappings
Gene2Symbol-method	Gene-to-symbol mappings
geneNames	Gene names
geneNames-method	Gene names

-- H --

headtail	Return the first and last parts of an object
headtail-method	Return the first and last parts of an object
humanize	Humanize an R object
humanize-method	Humanize an R object

-- I --

importSampleData	Import sample metadata
integerCounts	Integer counts
integerCounts-method	Integer counts
interestingGroups	Interesting groups
interestingGroups-method	Interesting groups
interestingGroups<-	Interesting groups
interestingGroups<--method	Interesting groups

-- M --

makeSampleData	Make sample data
makeSampleData-method	Make sample data
makeSummarizedExperiment	Make a SummarizedExperiment object
mapGenes	Map genes
mapGenesToIDs	Map genes
mapGenesToIDs-method	Map genes
mapGenesToRownames	Map genes
mapGenesToRownames-method	Map genes
mapGenesToSymbols	Map genes
mapGenesToSymbols-method	Map genes
matchInterestingGroups	Match interesting groups
matchSampleColumn	Match sample identifier column
matchSampleColumn-method	Match sample identifier column
melt	Melt columns into key-value pairs
melt-method	Melt columns into key-value pairs
metrics	Quality control metrics
metrics-method	Quality control metrics
microplate	Microtiter plate well identifiers
minimalSampleData	Minimal sample data

-- N --

nonzeroRowsAndCols	Subset object to keep only non-zero rows and columns
nonzeroRowsAndCols-method	Subset object to keep only non-zero rows and columns

-- O --

organism	Organism
organism-method	Organism
organism<-	Organism

-- S --

sampleData	Sample data
sampleData-method	Sample data
sampleData<-	Sample data
sampleData<--method	Sample data
sampleNames	Sample names
sampleNames-method	Sample data
sampleNames<-	Sample names
sampleNames<--method	Sample names
sanitizeSampleData	Sanitize sample data
selectSamples	Select samples
selectSamples-method	Select samples
sizeFactors	Size factors
sizeFactors-method	Size factors
sizeFactors<-	Size factors
sizeFactors<--method	Size factors
snakeCase	Syntactic naming functions
snakeCase-method	Syntactic naming functions
stripGeneVersions	Strip gene identifier versions
stripGeneVersions-method	Strip gene identifier versions
stripTranscriptVersions	Strip transcript identifier versions
stripTranscriptVersions-method	Strip transcript identifier versions
syntactic	Syntactic naming functions

-- T --

tpm	Transcripts per million
tpm-method	Transcripts per million
Tx2Gene	Transcript-to-gene identifier mappings
Tx2Gene-method	Transcript-to-gene identifier mappings

-- U --

uniteInterestingGroups	Unite interesting groups into a single column
uniteInterestingGroups-method	Unite interesting groups into a single column
upperCamelCase	Syntactic naming functions
upperCamelCase-method	Syntactic naming functions