# Base Functions for Bioinformatics

## Documentation for package ‘basejump’ version 0.7.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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

basejump-package | basejump

## -- A --

aggregateFeatures | Aggregate Features
aggregateFeatures-method | Aggregate Features
aggregateReplicates | Aggregate Replicates
aggregateReplicates-method | Aggregate Replicates
annotable | Ensembl Annotations
as | Methods for Coercing an Object to a Class
assertAllAreNonExisting | Assert All Variables Are Non-Existing
assertAreGeneAnnotations | Assert Are Ensembl Gene Annotations
assertAreTranscriptAnnotations | Assert Are Ensembl Transcript Annotations
assertFormalCompress | Assert Formal Compression
assertFormalGene2symbol | Assert Formal Gene to Symbol Mappings
assertFormalInterestingGroups | Interesting Groups Formal Assert Check
assertHasRownames | Assert Has Rownames
assertIsAHeaderLevel | Assert Is a Header Level
assertIsAnImplicitInteger | Assert Is Implicit Integer
assertIsAnImplicitIntegerOrNULL | Assert Is Implicit Integer
assertIsAnIntegerOrNULL | Assert Is an Integer or NULL
assertIsANumberOrNULL | Assert Is a Number or NULL
assertIsAStringOrNULL | Assert Is a String or NULL
assertIsCharacterOrNULL | Assert Is Character Vector or NULL
assertIsColorScaleContinuousOrNULL | Assert Is Color Palette Scale Continuous or NULL
assertIsColorScaleDiscreteOrNULL | Assert Is Color Palette Scale Discrete or NULL
assertIsDataFrameOrNULL | Assert Is Data Frame or NULL
assertIsFillScaleContinuousOrNULL | Assert Is Fill Palette Scale Continuous or NULL
assertIsFillScaleDiscreteOrNULL | Assert Is Fill Palette Scale Discrete or NULL
assertIsGene2symbol | Assert Is Gene to Symbol Mapping Data Frame
assertIsHexColorFunctionOrNULL | Assert Is Hex Color Function or NULL
assertIsImplicitInteger | Assert Is Implicit Integer
assertIsImplicitIntegerOrNULL | Assert Is Implicit Integer
assertIsTx2gene | Assert Is Transcript-to-Gene Mapping Data
assertIsURL | Assert Is URL
assignAndSaveData | Assign and Save Data

## -- B --

basejump | basejump
broadClass | Broad Class Definitions
broadClass-method | Broad Class Definitions

## -- C --

camel | Make Syntactically Valid Names
camel-method | Make Syntactically Valid Names
cleanSystemLibrary | Check for Clean System Library
coerce | Methods for Coercing an Object to a Class
coerce-method | Methods for Coercing an Object to a Class
collapseToString | Collapse to String
collapseToString-method | Collapse to String
convertGenesToSymbols | Convert Ensembl Identifiers to Gene Symbols
convertGenesToSymbols-method | Convert Ensembl Identifiers to Gene Symbols
convertSymbolsToGenes | Convert Ensembl Identifiers to Gene Symbols
convertSymbolsToGenes-method | Convert Ensembl Identifiers to Gene Symbols
convertTranscriptsToGenes | Convert Ensembl Transcripts to Genes
convertTranscriptsToGenes-method | Convert Ensembl Transcripts to Genes
convertUCSCBuildToEnsembl | Convert UCSC Build to Ensembl
counts | Counts
counts-method | Counts

## -- D --

detectHPC | Detect HPC Environment
detectOrganism | Detect Organism
detectOrganism-method | Detect Organism
dots | Extract Dots from Function
dotted | Make Syntactically Valid Names
dotted-method | Make Syntactically Valid Names

## -- E --

eggnog | EggNOG Annotations
emptyRanges | Generate Empty Genomic Ranges

## -- F --

fixNA | Fix Character Strings Missing 'NA'
fixNA-method | Fix Character Strings Missing 'NA'
flatFiles | Flat Files from S4 Object
flatFiles-method | Flat Files from S4 Object
foldChangeToLogRatio | Interconvert Log Ratio and Fold Change Values
foldChangeToLogRatio-method | Interconvert Log Ratio and Fold Change Values

## -- G --

gene2symbol | Gene to Symbol Mappings
gene2symbol-method | Gene to Symbol Mappings
geneSynonyms | Gene Synonyms
geometricMean | Geometric Mean
geometricMean-method | Geometric Mean
grepString | 'grep' String

## -- H --

hasRownames | Assert Has Rownames
hgnc2gene | HGNC to Ensembl Gene ID Mappings

## -- I --

initializeDirectory | Initialize Directory
interestingGroups | Interesting Groups
interestingGroups-method | Interesting Groups
interestingGroups<- | Interesting Groups
interestingGroups<--method | Interesting Groups
isAnImplicitInteger | Assert Is Implicit Integer
isImplicitInteger | Assert Is Implicit Integer
isURL | Assert Is URL

## -- K --

kables | Create Multiple Tables in LaTeX, HTML, Markdown and reStructuredText

## -- L --

loadData | Load Data
loadDataAsName | Load Data as Name
loadRemoteData | Load Remote Data
localOrRemoteFile | Dynamically Handle a Local or Remote File Path
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 --

makeGene2symbolFromEnsembl | Gene-to-Symbol Mappings from Ensembl
makeGene2symbolFromGFF | Gene-to-Symbol Mappings from GFF File
makeGene2symbolFromGTF | Gene-to-Symbol Mappings from GFF File
makeGRangesFromEnsembl | Genomic Ranges from Ensembl
makeGRangesFromGFF | Genomic Ranges from GFF File
makeGRangesFromGTF | Genomic Ranges from GFF File
makeNames | Make Syntactically Valid Names
makeSummarizedExperiment | Make Summarized Experiment
makeTx2geneFromEnsembl | Transcript-to-Gene Mappings from Ensembl
makeTx2geneFromGFF | Transcript-to-Gene Mappings from GFF File
makeTx2geneFromGTF | Transcript-to-Gene Mappings from GFF File
markdownHeader | Markdown Header
markdownLink | Markdown Link
markdownList | Markdown List
markdownPlotlist | Markdown Plotlist
matchInterestingGroups | Match Interesting Groups
mdHeader | Markdown Header
mdLink | Markdown Header
mdList | Markdown List
mdPlotlist | Markdown Plotlist
methodFormals | Access to the Formal Arguments of an S4 Method
mgi2gene | MGI to Ensembl Gene ID Mappings
microplate | Microtiter Plate Well Identifiers
multiassignAsEnvir | Assign Multiple Objects as an Environment

## -- P --

panther | PANTHER Gene Ontology Annotations
plotCorrelationHeatmap | Plot Correlation Heatmap
plotCorrelationHeatmap-method | Plot Correlation Heatmap
plotHeatmap | Plot Heatmap
plotHeatmap-method | Plot Heatmap
plotQuantileHeatmap | Plot Heatmap with Quantile Breaks
plotQuantileHeatmap-method | Plot Heatmap with Quantile Breaks
prepareTemplate | Prepare R Markdown Template File
printString | Print String

## -- R --

readFileByExtension | Read File by Extension
readGFF | Read GFF Annotations
readGTF | Read GFF Annotations
readJSON | Read JSON File
readYAML | Read YAML File
removeNA | Remove Rows and Columns Containing Only 'NA' Values
removeNA-method | Remove Rows and Columns Containing Only 'NA' Values
rnaseqCounts | Example RNA-Seq Counts
rnaseq_counts | Example RNA-Seq Counts
rse_bcb | 'RangedSummarizedExperiment' Coerced from 'bcbioRNASeq'
rse_dds | 'RangedSummarizedExperiment' Coerced from 'DESeqDataSet'

## -- S --

sampleData | Sample Data
sampleData-method | Sample Data
sampleData<- | Sample Data
sampleData<--method | Sample Data
sampleNames | Sample Names
sampleNames-method | Sample Data
sanitizeRowData | Sanitize Row Data
sanitizeSampleData | Sanitize Sample Data
saveData | Save Data
selectSamples | Select Samples
selectSamples-method | Select Samples
singleCellCounts | Example Single-Cell RNA-Seq Counts
single_cell_counts | Example Single-Cell RNA-Seq Counts
snake | Make Syntactically Valid Names
snake-method | Make Syntactically Valid Names
sortUnique | Sort and Make Unique
stripTranscriptVersions | Strip Transcript Versions
stripTranscriptVersions-method | Strip Transcript Versions

## -- T --

themes | Complete Themes
theme_midnight | Complete Themes
theme_paperwhite | Complete Themes
toStringUnique | Convert to a Unique Character String
transmit | Transmit Files from a Remote FTP Server

## -- U --

uniteInterestingGroups | Unite Interesting Groups
uniteInterestingGroups-method | Unite Interesting Groups
upperCamel | Make Syntactically Valid Names
upperCamel-method | Make Syntactically Valid Names

## -- W --

writeCounts | Write Counts