Package index

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