Package Information

basejump-package

basejump

Data Functions

aggregateFeatures()

Aggregate Features

aggregateReplicates()

Aggregate Replicates

counts(<SummarizedExperiment>)

Counts

flatFiles()

Flat Files from S4 Object

interestingGroups() `interestingGroups<-`()

Interesting Groups

makeSummarizedExperiment()

Make Summarized Experiment

sampleData() `sampleData<-`() sampleNames(<SummarizedExperiment>)

Sample Data

sampleNames

Sample Names

selectSamples()

Select Samples

Annotation Functions

annotable()

Ensembl Annotations

broadClass()

Broad Class Definitions

convertGenesToSymbols() convertSymbolsToGenes()

Convert Ensembl Identifiers to Gene Symbols

convertTranscriptsToGenes()

Convert Ensembl Transcripts to Genes

convertUCSCBuildToEnsembl()

Convert UCSC Build to Ensembl

eggnog()

EggNOG Annotations

emptyRanges()

Generate Empty Genomic Ranges

gene2symbol()

Gene to Symbol Mappings

geneSynonyms()

Gene Synonyms

hgnc2gene()

HGNC to Ensembl Gene ID Mappings

makeGene2symbolFromEnsembl()

Gene-to-Symbol Mappings from Ensembl

makeGene2symbolFromGFF()

Gene-to-Symbol Mappings from GFF File

makeGRangesFromEnsembl()

Genomic Ranges from Ensembl

makeGRangesFromGFF()

Genomic Ranges from GFF File

makeTx2geneFromEnsembl()

Transcript-to-Gene Mappings from Ensembl

makeTx2geneFromGFF()

Transcript-to-Gene Mappings from GFF File

mgi2gene()

MGI to Ensembl Gene ID Mappings

stripTranscriptVersions()

Strip Transcript Versions

panther()

PANTHER Gene Ontology Annotations

Plot Functions

plotCorrelationHeatmap()

Plot Correlation Heatmap

plotHeatmap()

Plot Heatmap

plotQuantileHeatmap()

Plot Heatmap with Quantile Breaks

Read/Write Functions

assignAndSaveData()

Assign and Save Data

loadData()

Load Data

loadDataAsName()

Load Data as Name

loadRemoteData()

Load Remote Data

readFileByExtension()

Read File by Extension

readGFF()

Read GFF Annotations

readJSON()

Read JSON File

readYAML()

Read YAML File

saveData()

Save Data

transmit()

Transmit Files from a Remote FTP Server

writeCounts()

Write Counts

Math and Science Functions

foldChangeToLogRatio() logRatioToFoldChange()

Interconvert Log Ratio and Fold Change Values

geometricMean()

Geometric Mean

microplate()

Microtiter Plate Well Identifiers

Plot Functions

theme_midnight() theme_paperwhite()

Complete Themes

R Markdown Functions

kables()

Create Multiple Tables in LaTeX, HTML, Markdown and reStructuredText

markdownHeader()

Markdown Header

markdownLink()

Markdown Link

markdownList()

Markdown List

markdownPlotlist()

Markdown Plotlist

Sanitization Functions

fixNA()

Fix Character Strings Missing NA

camel() dotted() snake() upperCamel() makeNames()

Make Syntactically Valid Names

removeNA()

Remove Rows and Columns Containing Only NA Values

sanitizeRowData()

Sanitize Row Data

sanitizeSampleData()

Sanitize Sample Data

Atomic Vector Functions

collapseToString()

Collapse to String

grepString()

grep String

sortUnique()

Sort and Make Unique

toStringUnique()

Convert to a Unique Character String

Coercion Methods

coerce

Methods for Coercing an Object to a Class

Developer Functions

detectHPC()

Detect HPC Environment

detectOrganism()

Detect Organism

dots()

Extract Dots from Function

initializeDirectory()

Initialize Directory

localOrRemoteFile()

Dynamically Handle a Local or Remote File Path

matchInterestingGroups()

Match Interesting Groups

methodFormals()

Access to the Formal Arguments of an S4 Method

multiassignAsEnvir()

Assign Multiple Objects as an Environment

printString()

Print String

uniteInterestingGroups()

Unite Interesting Groups

Assert Check Functions

Readable check functions to ensure code integrity.

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() hasRownames()

Assert Has Rownames

assertIsAHeaderLevel()

Assert Is a Header Level

assertIsANumberOrNULL()

Assert Is a Number or NULL

assertIsAStringOrNULL()

Assert Is a String or NULL

assertIsAnIntegerOrNULL()

Assert Is an Integer 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

assertIsAnImplicitInteger() assertIsAnImplicitIntegerOrNULL() assertIsImplicitInteger() assertIsImplicitIntegerOrNULL() isAnImplicitInteger() isImplicitInteger()

Assert Is Implicit Integer

assertIsTx2gene()

Assert Is Transcript-to-Gene Mapping Data

assertIsURL() isURL()

Assert Is URL

Example Datasets

rnaseq_counts

Example RNA-Seq Counts

rse_bcb

RangedSummarizedExperiment Coerced from bcbioRNASeq

rse_dds

RangedSummarizedExperiment Coerced from DESeqDataSet

single_cell_counts

Example Single-Cell RNA-Seq Counts