Acid Genomics Base Functions

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Documentation for package ‘AcidBase’ version 0.6.8

• DESCRIPTION file.

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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
decompress	Compress or decompress a file
dots	Extract dots from function
download	Download a file from the Internet
fileDepth	File depth
fileExt	File extension
foldChangeToLogRatio	Interconvert log ratio and fold change values
foldChangeToLogRatio-method	Interconvert log ratio and fold change values
forceDetach	Force detach packages
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
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
majorVersion	Major version
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	Minor version
missingOrNULL-class	Missing or NULL class union
modifyPathString	System path string handlers
params	Shared parameter documentation
parentDir	Parent directory recursion
parentDirectory	Parent directory recursion
pasteURL	Concatenate strings to form a URL
printString	Print string
rankedMatrix	Calculate a ranked matrix
rankedMatrix-method	Calculate a ranked matrix
realpath	Express file paths in canonical form
removeFromPath	System path string handlers
requireNamespaces	Require package namespaces
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
tempdir2	Unique temporary directory
truncateString	Truncate a string with ellipsis, if necessary
uniquePathString	Unique path string
unlink2	Delete files and directories
updateMessage	Update message