Acid Genomics Summarized Experiment

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Documentation for package ‘AcidExperiment’ version 0.5.4

• DESCRIPTION file.
• Package NEWS.

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	Coerce to 'SummarizedExperiment'.
as.SummarizedExperiment-method	Coerce to 'SummarizedExperiment'.
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
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
droplevels2	Drop unused levels from factors
droplevels2-method	Drop unused levels from factors

-- E --

encode	Encode using run-length encoding
encode-method	Encode using run-length encoding
EnsemblToNcbi	Ensembl-to-NCBI gene identifier mappings
EnsemblToNcbi-method	Ensembl-to-NCBI gene identifier mappings
estimateSizeFactors	Define size factors from the library sizes, and then apply centering at unity. This ensures that the library size adjustment yields values comparable to those generated after normalization with other sets of size factors.
estimateSizeFactors-method	Define size factors from the library sizes, and then apply centering at unity. This ensures that the library size adjustment yields values comparable to those generated after normalization with other sets of size factors.
export	Export data from R
export-method	Export data from R

-- G --

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

-- 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 data from wide to long format
melt-method	Melt data from wide to long format
metrics	Quality control metrics
metrics-method	Quality control metrics
microplate	Microtiter plate well identifiers
minimalSampleData	Minimal sample data

-- N --

NcbiToEnsembl	Ensembl-to-NCBI gene identifier mappings
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
TxToGene	Transcript-to-gene mappings
TxToGene-method	Transcript-to-gene 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