# Base functions for bioinformatics

## Documentation for package ‘basejump’ version 0.9.11

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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-method | Aggregate rows or columns
aggregateRows-method | Aggregate rows or columns
annotable | Make a 'GenomicRanges' object
autopadZeros | Autopad zeros
autopadZeros-method | Autopad zeros

## -- B --

barcodePattern | Single-sell barcode pattern
basejump_geom_abline | ggplot2 geometric objects
basejump_geom_label | ggplot2 geometric objects
basejump_geom_label_average | ggplot2 geometric objects
basejump_geom_label_repel | ggplot2 geometric objects

## -- C --

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-method | Convert genes to symbols
convertTranscriptsToGenes | Convert transcripts to genes
convertTranscriptsToGenes-method | Convert transcripts to genes
convertUCSCBuildToEnsembl | Convert UCSC build to Ensembl
counts | Counts
counts-method | Counts
counts<- | Counts
counts<--method | Counts

## -- D --

detectHPC | Detect HPC environment
detectLanes | Detect sequencing lanes
detectOrganism | Detect organism
df | Example 'DataFrame'

## -- E --

EggNOG | EggNOG database annotations
EggNOG-class | EggNOG database annotations
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

## -- F --

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

## -- G --

gender_markers | Sexually dimorphic gender marker genes
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
ggplot2-geoms | ggplot2 geometric objects
ggplot2-themes | ggplot2 themes

## -- 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<--method | Interesting groups

## -- L --

lanePattern | Sequencing lane grep pattern
logRatio | 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
makeGRanges | Make a 'GenomicRanges' object
makeGRangesFromEnsDb | Make a 'GenomicRanges' object
makeGRangesFromEnsembl | Make a 'GenomicRanges' object
makeGRangesFromGFF | Make a 'GenomicRanges' object
makeGRangesFromGTF | Make a 'GenomicRanges' object
makeSampleData | Make sample data
makeSingleCellExperiment | Make a 'SingleCellExperiment' object
makeSummarizedExperiment | 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-method | Map genes
mapGenesToRownames-method | 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
mat | Example 'matrix'
matchesGene2Symbol | Check that user-defined gene input matches expected values
matchesInterestingGroups | Check that interesting groups match a defined value
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
metrics | Quality control metrics
metrics-method | 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_mappings | Organism mappings

## -- P --

PANTHER | PANTHER database annotations
PANTHER-class | PANTHER database annotations
plotCorrelationHeatmap | Correlation heatmap
plotCorrelationHeatmap-method | Correlation heatmap
plotCounts | Plot counts
plotCounts-method | Plot counts
plotCountsPerBiotype | Plot counts per biotype
plotCountsPerBiotype-method | Plot counts per biotype
plotCountsPerBroadClass | Plot counts per broad class definition
plotCountsPerBroadClass-method | Plot counts per biotype
plotCountsPerGene | Plot counts per gene
plotCountsPerGene-method | Plot counts per gene
plotGenderMarkers | Plot sexually dimorphic gender marker genes
plotGenderMarkers-method | Plot sexually dimorphic gender marker genes
plotGenesDetected | Plot genes detected
plotGenesDetected-method | Plot genes detected
plotHeatmap | Heatmap
plotHeatmap-method | Heatmap
plotPCA | Principal component analysis plot
plotPCA-method | Principal component analysis plot
plotQC | Quality control
plotQC-method | Quality control
plotQuantileHeatmap | Quantile heatmap
plotQuantileHeatmap-method | Quantile heatmap
plotTotalCounts | Plot total read counts
plotTotalCounts-method | Plot total read counts
plotZerosVsDepth | Plot percentage of zeros vs. library depth
plotZerosVsDepth-method | Plot percentage of zeros vs. library depth
prepareTemplate | Prepare R Markdown template

## -- R --

relevel | Relevel row or column data
relevelColData | Relevel row or column data
relevelRowRanges | Relevel row or column data
removeNA | Remove rows and columns containing only 'NA' values
removeNA-method | Remove rows and columns containing only 'NA' values
rse | Example 'SummarizedExperiment'

## -- S --

sampleData | Sample data
sampleData-method | Sample data
sampleData<--method | Sample data
sampleNames | Sample names
sampleNames-method | Sample data
sampleNames<- | Sample names
sampleNames<--method | Sample names
sanitizeNA | Sanitize 'NA' values
sanitizeNA-method | Sanitize 'NA' values
sanitizePercent | Sanitize percentage
sanitizePercent-method | Sanitize percentage
sanitizeSampleData | Sanitize sample data
sce | Example 'SingleCellExperiment'
selectSamples | Select samples
selectSamples-method | Select samples
separator | Separator bar
show | Show an object
show-method | Show an object
showSlotInfo | Show slot information
sortUnique | Sort and make unique
sparse | Example 'sparseMatrix'
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 --

tbl | Example 'tibble' ('tbl_df')
theme_midnight | ggplot2 themes
theme_paperwhite | ggplot2 themes
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
tx_se | Example transcript-level 'SummarizedExperiment'

## -- 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