Man pages for acidgenomics/AcidBase
Acid Genomics Base Functions
| AcidBase-package | AcidBase |
| 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 | 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 | Extract duplicated values |
| euclidean | Calculate Euclidean distance |
| fileDepth | File depth |
| fileExt | File extension |
| genomeMetadataNames | Slot names in metadata containing genome information |
| geometricMean | Geometric mean |
| gitBranch | 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 |
| logRatio | Interconvert log ratio and fold change values |
| majorMinorVersion | Major and minor version |
| majorVersion | Major version |
| matchAll | Match all positions of an argument |
| matchNested | Match inside nested elements |
| metadataDenylist | Sample metadata denylist |
| methodDefinition | Access the data inside an S4 method definition |
| metricsCols | Quality control metric columns |
| missingOrNULL-class | Missing or NULL class union |
| modifyPathString | System path string handlers |
| params | Shared parameter documentation |
| 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 |
| realpath | Express file paths in canonical form |
| reexports | Objects exported from other packages |
| 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 |
