Acid Genomics Base Functions

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Documentation for package ‘AcidBase’ version 0.7.3

• DESCRIPTION file.
• Package NEWS.

Help Pages

addToPathEnd	System path string handlers
addToPathStart	System path string handlers
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
coerceToList-method	Coerce to list
collapseToPathString	Collapse the input to a 'PATH' string.
compress	Compress or decompress a file
cpus	Detect the number of CPU cores
decompress	Compress or decompress a file
dots	Extract dots from function
download	Download a file from the Internet
dupes	Extract duplicated values
euclidean	Calculate Euclidean distance
euclidean-method	Calculate Euclidean distance
fileDepth	File depth
fileExt	File extension
foldChangeToLogRatio	Interconvert log ratio and fold change values
foldChangeToLogRatio-method	Interconvert log ratio and fold change values
genomeMetadataNames	Slot names in metadata containing genome information
geometricMean	Geometric mean
geometricMean-method	Geometric mean
gitBranch	Git branch strings
gitCurrentBranch	Git branch strings
gitDefaultBranch	Git branch strings
headtail	Return the first and last parts of an object
headtail-method	Return the first and last parts of an object
initDir	Initialize directory
intersectAll	Intersection of more than two vectors
intersectAll-method	Intersection of more than two vectors
intersectionMatrix	Intersection matrix
intersectionMatrix-method	Intersection matrix
keepOnlyAtomicCols	Keep only atomic columns
keepOnlyAtomicCols-method	Keep only atomic columns
lanePattern	Sequencing lane grep pattern
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
majorMinorVersion	Major and minor version
majorVersion	Major version
matchAll	Match all positions of an argument
matchAll-method	Match all positions of an argument
matchNested	Match inside nested elements
matchNested-method	Match inside nested elements
metadataDenylist	Sample metadata denylist
methodDefinition	Access the data inside an S4 method definition
methodFormals	Access the data inside an S4 method definition
methodFunction	Access the data inside an S4 method definition
metricsCols	Quality control metric columns
minorVersion	Major and minor version
missingOrNULL-class	Missing or NULL class union
modifyPathString	System path string handlers
notDupes	Extract duplicated values
params	Shared parameter documentation
parentDir	Parent directory recursion
parentDirectory	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
rankedMatrix-method	Calculate a ranked matrix
realpath	Express file paths in canonical form
removeFromPath	System path string handlers
sanitizeVersion	Sanitize version
sem	Standard error of the mean
sem-method	Standard error of the mean
shell	Invoke a command in the system command-line shell
showHeader	Header for object show method
showHeader-method	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
zscore-method	Calculate Z-score