Function reference • AcidBase

All functions

appendToBody(): Append values to function body

barcodePattern: Single-sell barcode pattern

basenameSansExt(): Base name without the file extension

classContains(): Get the class contained in a specificed class definition

coerceToList(): Coerce to list

collapseToPathString(): Collapse the input to a PATH string.

compress() decompress(): Compress or decompress a file

cpus(): Detect the number of CPU cores

dots(): Extract dots from function

download(): Download a file from the Internet

dupes() notDupes(): Extract duplicated values

euclidean(): Calculate Euclidean distance

fileDepth(): File depth

fileExt(): File extension

genomeMetadataNames: Slot names in metadata containing genome information

geometricMean(): Geometric mean

gitCurrentBranch() gitDefaultBranch(): Git branch strings

headtail(): Return the first and last parts of an object

initDir(): Initialize directory

intersectAll(): Intersection of more than two vectors

intersectionMatrix(): Intersection matrix

keepOnlyAtomicCols(): Keep only atomic columns

lanePattern: Sequencing lane grep pattern

foldChangeToLogRatio() logRatioToFoldChange(): Interconvert log ratio and fold change values

majorMinorVersion() minorVersion(): Major and minor version

majorVersion(): Major version

matchAll(): Match all positions of an argument

matchNested(): Match inside nested elements

metadataDenylist: Sample metadata denylist

methodFunction() methodFormals(): Access the data inside an S4 method definition

metricsCols: Quality control metric columns

missingOrNULL-class: Missing or NULL class union

addToPathEnd() addToPathStart() removeFromPath(): System path string handlers

params: Shared parameter documentation

parentDirectory() parentDir(): Parent directory recursion

pasteUrl(): Concatenate strings to form a URL

pkgCacheDir(): Create a local cache directory for a package

printString(): Print string

ram(): Return system random access memory (RAM) information

randomString(): Generate a random string

rankedMatrix(): Calculate a ranked matrix

realpath(): Express file paths in canonical form

sanitizeVersion(): Sanitize version

sem(): Standard error of the mean

shell(): Invoke a command in the system command-line shell

showHeader(): Header for object show method

showSlotInfo(): Show slot information

simpleClass(): Simple class of object

splitPathString(): Split path string environment variable

standardizeCall(): Standardize call

strExtract(): Extract first pattern occurance

strExtractAll(): Extract all pattern occurances

strMatch(): Extract components from first match

strMatchAll(): Extract components from all matches

strPad(): Pad a string to minimum width

strRemoveEmpty(): Remove empty strings

strReplaceNa(): Replace NA with "NA"

strSplit(): Split the elements of a character vector into a matrix

tempdir2(): Unique temporary directory

truncateString(): Truncate a string with ellipsis, if necessary

uniquePathString(): Unique path string

unlink2(): Delete files and directories

updateMessage: Update message

zscore(): Calculate Z-score