Base Functions for Bioinformatics

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Documentation for package ‘basejump’ version 0.7.2

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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