Package index • AcidBase

Constants

barcodePattern: Single-sell barcode pattern
lanePattern: Sequencing lane grep pattern
genomeMetadataNames: Slot names in metadata containing genome information
metadataDenylist: Sample metadata denylist
metricsCols: Quality control metric columns
updateMessage: Update message

Math and statistics

euclidean(): Calculate Euclidean distance
foldChangeToLogRatio() logRatioToFoldChange(): Interconvert log ratio and fold change values
geometricMean(): Geometric mean
headtail(): Return the first and last parts of an object
intersectAll(): Intersection of more than two vectors
intersectionMatrix(): Intersection matrix
rankedMatrix(): Calculate a ranked matrix
sem(): Standard error of the mean
zscore(): Calculate Z-score

Data manipulation

dupes() notDupes(): Extract duplicated values
keepOnlyAtomicCols(): Keep only atomic columns
matchAll(): Match all positions of an argument
matchNested(): Match inside nested elements

String utilities

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

File and path utilities

basenameSansExt(): Base name without the file extension
compress() decompress(): Compress or decompress a file
fileDepth(): File depth
fileExt(): File extension
initDir(): Initialize directory
parentDirectory() parentDir(): Parent directory recursion
realpath(): Express file paths in canonical form
tempdir2(): Unique temporary directory
unlink2(): Delete files and directories

Path string manipulation

addToPathEnd() addToPathStart() removeFromPath(): System path string handlers
collapseToPathString(): Collapse the input to a PATH string.
splitPathString(): Split path string environment variable
uniquePathString(): Unique path string

System utilities

cpus(): Detect the number of CPU cores
gitCurrentBranch() gitDefaultBranch(): Git branch strings
reexports quietly: Objects exported from other packages
ram(): Return system random access memory (RAM) information
randomString(): Generate a random string
shell(): Invoke a command in the system command-line shell

Version utilities

majorMinorVersion() minorVersion(): Major and minor version
majorVersion(): Major version
sanitizeVersion(): Sanitize version

Download and URL

download(): Download a file from the Internet
pasteUrl(): Concatenate strings to form a URL

Display and S4 helpers

showHeader(): Header for object show method
showSlotInfo(): Show slot information
simpleClass(): Simple class of object
pkgCacheDir(): Create a local cache directory for a package

Metaprogramming

appendToBody(): Append values to function body
classContains(): Get the class contained in a specificed class definition
coerceToList(): Coerce to list
methodFunction() methodFormals(): Access the data inside an S4 method definition
standardizeCall(): Standardize call

Internal

dots(): Extract dots from function
missingOrNULL-class: Missing or NULL class union
params: Shared parameter documentation