Base Functions for Bioinformatics


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Documentation for package ‘basejump’ version 0.11.23

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A B C D E F G H I L M N O P R S T U W 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
camelCase Camel case
camelCase-method Camel case
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
correlation Correlation
correlation-method Correlation
counts Counts
counts-method Counts
counts<- Counts
counts<--method Counts

-- D --

detectHPC Detect HPC environment
detectLanes Detect sequencing lanes
dottedCase Dotted case
dottedCase-method Dotted case

-- E --

Ensembl2Entrez Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-class Ensembl-to-Entrez gene identifier mappings
Ensembl2Entrez-method Ensembl-to-Entrez gene identifier mappings
ensemblVersion Genome versions
estimateSizeFactors Estimate size factors
estimateSizeFactors-method Estimate size factors

-- F --

filterCells Filter cells
filterCells-method Filter cells
flybaseVersion Genome versions
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 --

gencodeVersion Genome versions
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
genomeVersions Genome versions
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 --

importSampleData Import sample metadata
importTx2Gene Import transcript-to-gene annotations
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
makeTx2GeneFromFASTA Make a Tx2Gene object from transcriptome FASTA
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
mcolnames Metadata column names
mcolnames-method Metadata column names
mcolnames<- Metadata column names
mcolnames<--method Metadata column names
mdHeader Markdown header
mdLink Markdown hyperlink
mdList Markdown list
mdPlots Multiple Markdown plots
mdTables Multiple Markdown tables
melt Melt columns into key-value pairs
melt-method Melt columns into key-value pairs
metadataBlacklist Sample metadata blacklist
metrics Quality control metrics
metrics-method Quality control metrics
metricsCols Quality control metric columns
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

-- 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
organism<--method Organism

-- P --

prepareTemplate Prepare R Markdown template
pseudobulk Pseudobulk
pseudobulk-method Pseudobulk

-- R --

rankedMatrix Calculate a ranked matrix
refseqVersion Genome versions

-- 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
showHeader Header for object show method
showSlotInfo Show slot information
sizeFactors Size factors
sizeFactors-method Size factors
sizeFactors<- Size factors
sizeFactors<--method Size factors
snakeCase Snake case
snakeCase-method Snake case
sortUnique Sort and make unique
stripGeneVersions Strip transcript versions
stripTranscriptVersions Strip transcript versions
stripTranscriptVersions-method Strip transcript versions
subsetPerSample Subset per sample
subsetPerSample-method Subset per sample

-- 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
upperCamelCase Upper camel case
upperCamelCase-method Upper camel case

-- W --

wormbaseVersion Genome versions

-- Z --

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