Man pages for acidgenomics/AcidBase
Acid Genomics Base Functions

appendToBodyAppend values to function body
barcodePatternSingle-sell barcode pattern
basenameSansExtBase name without the file extension
classContainsGet the class contained in a specificed class definition
coerceToListCoerce to list
collapseToPathStringCollapse the input to a 'PATH' string.
compressCompress or decompress a file
cpusDetect the number of CPU cores
dotsExtract dots from function
downloadDownload a file from the Internet
dupesExtract duplicated values
euclideanCalculate Euclidean distance
fileDepthFile depth
fileExtFile extension
genomeMetadataNamesSlot names in metadata containing genome information
geometricMeanGeometric mean
gitBranchGit branch strings
headtailReturn the first and last parts of an object
initDirInitialize directory
intersectAllIntersection of more than two vectors
intersectionMatrixIntersection matrix
keepOnlyAtomicColsKeep only atomic columns
lanePatternSequencing lane grep pattern
logRatioInterconvert log ratio and fold change values
majorMinorVersionMajor and minor version
majorVersionMajor version
matchAllMatch all positions of an argument
matchNestedMatch inside nested elements
metadataDenylistSample metadata denylist
methodDefinitionAccess the data inside an S4 method definition
metricsColsQuality control metric columns
missingOrNULL-classMissing or NULL class union
modifyPathStringSystem path string handlers
paramsShared parameter documentation
parentDirectoryParent directory recursion
pasteUrlConcatenate strings to form a URL
pkgCacheDirCreate a local cache directory for a package
printStringPrint string
ramReturn system random access memory (RAM) information
randomStringGenerate a random string
rankedMatrixCalculate a ranked matrix
realpathExpress file paths in canonical form
reexportsObjects exported from other packages
sanitizeVersionSanitize version
semStandard error of the mean
shellInvoke a command in the system command-line shell
showHeaderHeader for object show method
showSlotInfoShow slot information
simpleClassSimple class of object
splitPathStringSplit path string environment variable
standardizeCallStandardize call
strExtractExtract first pattern occurance
strExtractAllExtract all pattern occurances
strMatchExtract components from first match
strMatchAllExtract components from all matches
strPadPad a string to minimum width
strRemoveEmptyRemove empty strings
strReplaceNaReplace 'NA' with '"NA"'
strSplitSplit the elements of a character vector into a matrix
tempdir2Unique temporary directory
truncateStringTruncate a string with ellipsis, if necessary
uniquePathStringUnique path string
unlink2Delete files and directories
updateMessageUpdate message
zscoreCalculate Z-score
acidgenomics/AcidBase documentation built on Jan. 28, 2024, 2:59 a.m.