# Base Functions for Bioinformatics

## Documentation for package ‘basejump’ version 0.12.4

- DESCRIPTION file.

## Help Pages

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

## -- A --

aggregate | Aggregate
aggregate-method | Aggregate
aggregateCellsToSamples | Aggregate cells to samples
aggregateCellsToSamples-method | Aggregate cells to samples
aggregateCols | Aggregate columns
aggregateCols-method | Aggregate columns
aggregateRows | Aggregate rows
aggregateRows-method | Aggregate rows
alphaThreshold | Alpha threshold
alphaThreshold-method | Alpha threshold
alphaThreshold<- | Alpha threshold
alphaThreshold<--method | Alpha threshold
annotable | Make GRanges from Ensembl
antiJoin | Join operations
antiJoin-method | Join operations
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
convertUCSCBuildToEnsembl | Convert UCSC build to Ensembl
correlation | Correlation
correlation-method | Correlation
counts | Counts
counts-method | Counts
counts<- | Counts
counts<--method | Counts
currentEnsemblVersion | Current genome version
currentFlybaseVersion | Current genome version
currentGencodeVersion | Current genome version
currentGenomeVersion | Current genome version
currentRefseqVersion | Current genome version
currentWormbaseVersion | Current genome version

## -- D --

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

## -- E --

emptyRanges | Generate empty genomic ranges
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
fullJoin | Join operations
fullJoin-method | Join operations

## -- 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
getURLDirList | Get remote URL directory listing

## -- 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
innerJoin | Join operations
innerJoin-method | Join operations
integerCounts | Integer counts
integerCounts-method | Integer counts
interestingGroups | Interesting groups
interestingGroups-method | Interesting groups
interestingGroups<- | Interesting groups
interestingGroups<--method | Interesting groups

## -- J --

join | Join operations

## -- L --

lanePattern | Sequencing lane grep pattern
leftJoin | Join operations
leftJoin-method | Join operations
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
makeGRangesFromEnsDb | Make GRanges from EnsDb object
makeGRangesFromEnsembl | Make GRanges from Ensembl
makeGRangesFromGFF | Make GRanges from a GFF/GTF file
makeGRangesFromGTF | Make GRanges from a GFF/GTF file
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
mutate | Mutate multiple columns
mutateAll | Mutate multiple columns
mutateAll-method | Mutate multiple columns
mutateAt | Mutate multiple columns
mutateAt-method | Mutate multiple columns
mutateIf | Mutate multiple columns
mutateIf-method | Mutate multiple columns

## -- 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

## -- R --

rankedMatrix | Calculate a ranked matrix
rightJoin | Join operations
rightJoin-method | Join operations

## -- 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
select | Select multiple columns
selectIf | Select multiple columns
selectIf-method | Select multiple columns
selectSamples | Select samples
selectSamples-method | Select samples
semiJoin | Join operations
semiJoin-method | Join operations
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
transmit | Transmit files from a remote FTP server
transmuteAt | Mutate multiple columns
transmuteAt-method | Mutate multiple columns
transmuteIf | Mutate multiple columns
transmuteIf-method | Mutate multiple columns
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

## -- Z --

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