Base Functions for Bioinformatics

Documentation for package ‘basejump’ version 0.13.2

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-- 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
autopadZeros	Autopad zeros
autopadZeros-method	Autopad zeros

-- 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
correlation	Correlation
correlation-method	Correlation
counts	Counts
counts-method	Counts
counts<-	Counts
counts<--method	Counts

-- D --

-- E --

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

-- G --

geometricMean	Geometric mean
geometricMean-method	Geometric mean

-- H --

headtail	Return the first and last parts of an object
headtail-method	Return the first and last parts of an object
humanize	Humanize an R object
humanize-method	Humanize an R object

-- I --

importSampleData	Import sample metadata
integerCounts	Integer counts
integerCounts-method	Integer counts
interestingGroups	Interesting groups
interestingGroups-method	Interesting groups
interestingGroups<-	Interesting groups
interestingGroups<--method	Interesting groups
intersectAll	Intersection of more than two vectors
intersectAll-method	Intersection of more than two vectors
intersectionMatrix	Intersection matrix
intersectionMatrix-method	Intersection matrix

-- L --

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 --

makeSampleData	Make sample data
makeSampleData-method	Make sample data
makeSingleCellExperiment	Make a SingleCellExperiment object
makeSummarizedExperiment	Make a SummarizedExperiment 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
matchesGene2Symbol	Check that user-defined gene input matches expected values
matchesInterestingGroups	Check that interesting groups match a defined value
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
metrics	Quality control metrics
metrics-method	Quality control metrics
metricsPerSample	Quality control metrics
metricsPerSample-method	Quality control metrics
microplate	Microtiter plate well identifiers
minimalSampleData	Minimal sample data
multiassignAsEnvir	Assign multiple objects into a new environment

-- N --

nonzeroRowsAndCols	Subset object to keep only non-zero rows and columns
nonzeroRowsAndCols-method	Subset object to keep only non-zero rows and columns

-- P --

Prepare R Markdown template

-- R --

Calculate a ranked matrix

-- 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
selectSamples	Select samples
selectSamples-method	Select samples
separator	Separator bar
showHeader	Header for object show method
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
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

-- 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