Base Functions for Bioinformatics

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Documentation for package ‘basejump’ version 0.11.8

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A B C D E F G H I L M O P R S T U Z

-- A --

aggregate Aggregate rows or columns
aggregateCellsToSamples Aggregate cells to samples
aggregateCellsToSamples-method Aggregate cells to samples
aggregateCols Aggregate rows or columns
aggregateCols-method Aggregate rows or columns
aggregateRows Aggregate rows or columns
aggregateRows-method Aggregate rows or columns
alphaThreshold Alpha threshold
alphaThreshold-method Alpha threshold
alphaThreshold<- Alpha threshold
alphaThreshold<--method Alpha threshold
autopadZeros Autopad zeros
autopadZeros-method Autopad zeros

-- B --

barcodePattern Single-sell barcode pattern

-- C --

calculateMetrics Calculate quality control metrics
calculateMetrics-method Calculate quality control metrics
cell2sample Cell-to-sample mappings
cell2sample-method Cell-to-sample mappings
collapseToString Collapse to string
collapseToString-method Collapse to string
combine Combining or merging different Bioconductor data structures
combine-method Combining or merging different Bioconductor data structures
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
counts Counts
counts-method Counts
counts<- Counts
counts<--method Counts

-- D --

detectHPC Detect HPC environment
detectLanes Detect sequencing lanes

-- E --

EggNOG EggNOG database annotations
EggNOG-class EggNOG database annotations
Ensembl2Entrez Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-class Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-method Ensembl-to-Entrez gene identifier mappings
estimateSizeFactors Estimate size factors
estimateSizeFactors-method Estimate size factors

-- F --

filterCells Filter cells
filterCells-method Filter cells
foldChangeToLogRatio Interconvert log ratio and fold change values
foldChangeToLogRatio-method Interconvert log ratio and fold change values
formalsList Shared list of optional default formals

-- G --

Gene2Symbol Gene-to-symbol mappings
Gene2Symbol-class Gene-to-symbol mappings
Gene2Symbol-method Gene-to-symbol mappings
geneNames Gene names
geneNames-method Gene names
geneSynonyms Gene synonyms
genomeMetadataNames Slot names in metadata containing genome information
geometricMean Geometric mean
geometricMean-method Geometric mean

-- H --

headtail Return the first and last parts of an object
headtail-method Return the first and last parts of an object
HGNC2Ensembl HGNC-to-Ensembl gene identifier mappings
HGNC2Ensembl-class HGNC-to-Ensembl gene identifier mappings
humanize Humanize an R object
humanize-method Humanize an R object

-- I --

interestingGroups Interesting groups
interestingGroups-method Interesting groups
interestingGroups<- Interesting groups
interestingGroups<--method Interesting groups

-- L --

lanePattern Sequencing lane grep pattern
lfcThreshold Log2 fold change threshold
lfcThreshold-method Log2 fold change threshold
lfcThreshold<- Log2 fold change threshold
lfcThreshold<--method Log2 fold change threshold
logRatio Interconvert log ratio and fold change values
logRatioToFoldChange Interconvert log ratio and fold change values
logRatioToFoldChange-method Interconvert log ratio and fold change values

-- M --

makeGene2Symbol Make a Gene2Symbol object
makeGene2SymbolFromEnsDb Make a Gene2Symbol object
makeGene2SymbolFromEnsembl Make a Gene2Symbol object
makeGene2SymbolFromGFF Make a Gene2Symbol object
makeGene2SymbolFromGTF Make a Gene2Symbol object
makeSampleData Make sample data
makeSampleData-method Make sample data
makeSingleCellExperiment Make a SingleCellExperiment object
makeSingleCellExperiment-method Make a SingleCellExperiment object
makeSummarizedExperiment Make a SummarizedExperiment object
makeSummarizedExperiment-method Make a SummarizedExperiment object
makeTx2Gene Make a Tx2Gene object
makeTx2GeneFromEnsDb Make a Tx2Gene object
makeTx2GeneFromEnsembl Make a Tx2Gene object
makeTx2GeneFromGFF Make a Tx2Gene object
makeTx2GeneFromGTF Make a Tx2Gene object
mapCellsToSamples Map cells to samples
mapGenes Map genes
mapGenesToIDs Map genes
mapGenesToIDs-method Map genes
mapGenesToRownames Map genes
mapGenesToRownames-method Map genes
mapGenesToSymbols Map genes
mapGenesToSymbols-method Map genes
markdown Markdown
markdown-method Markdown
markdownHeader Markdown header
markdownLink Markdown hyperlink
markdownList Markdown list
markdownPlots Multiple Markdown plots
markdownTables Multiple Markdown tables
matchEnsemblReleaseToURL Match Ensembl release to archive URL.
matchesGene2Symbol Check that user-defined gene input matches expected values
matchesInterestingGroups Check that interesting groups match a defined value
matchHumanOrthologs Match human gene orthologs
matchInterestingGroups Match interesting groups
mdHeader Markdown header
mdLink Markdown hyperlink
mdList Markdown list
mdPlots Multiple Markdown plots
mdTables Multiple Markdown tables
meltCounts Melt count matrix into long format
meltCounts-method Melt count matrix into long format
metadataBlacklist Sample metadata blacklist
metrics Quality control metrics
metrics-method Quality control metrics
metricsPerSample Quality control metrics
metricsPerSample-method Quality control metrics
MGI2Ensembl MGI-to-Ensembl gene identifier mappings
MGI2Ensembl-class MGI-to-Ensembl gene identifier mappings
microplate Microtiter plate well identifiers
minimalSampleData Minimal sample data
multiassignAsEnvir Assign multiple objects into a new environment

-- O --

organism Organism
organism-method Organism
organism<- Organism
organism<--method Organism

-- P --

PANTHER PANTHER database annotations
PANTHER-class PANTHER database annotations
prepareTemplate Prepare R Markdown template
pseudobulk Pseudobulk
pseudobulk-method Pseudobulk

-- R --

rankedMatrix Calculate a ranked matrix
readSampleData Read sample metadata
readTx2Gene Read transcript-to-gene annotations

-- 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
separator Separator bar
show Show an object
show-method Show an object
showHeader Header for object show method
showSlotInfo Show slot information
sizeFactors Size factors
sizeFactors-method Size factors
sizeFactors<- Size factors
sizeFactors<--method Size factors
sortUnique Sort and make unique
stripTranscriptVersions Strip transcript versions
stripTranscriptVersions-method Strip transcript versions
subsetPerSample Subset per sample
subsetPerSample-method Subset per sample
summary Object summaries
summary-method Object summaries

-- T --

topCellsPerSample Top cells per sample
topCellsPerSample-method Top cells per sample
toStringUnique Convert to a unique character string
tpm Transcripts per million
tpm-method Transcripts per million
Tx2Gene Transcript-to-gene identifier mappings
Tx2Gene-class 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

-- Z --

zerosVsDepth Percentage of zeros vs. library depth
zerosVsDepth-method Percentage of zeros vs. library depth