Man pages for ribiosUtils
Utilities from and Interface to the Bioinfo-C (BIOS) Library
| allIdentical | Testing whether several objects are all identical with each... |
| asNumMatrix | Convert string-valued data frame or matrix into a numeric... |
| assertColumnName | Assert whether the required column names exist |
| assertContrast | Check dimensionality of contrast matrix |
| assertDesign | Check dimensionality of design matrix |
| assertDesignContrast | Check dimensionality of both design and contrast matrix |
| bedaInfo | Print BEDA project information |
| biomicsPstorePath2URL | Translate BiOmics-Pathology pstore path to URL |
| checkFile | Check whether file(s) exist |
| chosenFew | Print the chosen few items of a long vector |
| closeLoggerConnections | Close connections to all loggers This function closes all... |
| columnOverlapCoefficient | Pairwise jaccard/overlap coefficient can be calculated... |
| compTwoVecs | Compare two vectors by set operations |
| countTokens | Count tokens by splitting strings |
| createDir | Create a directory if it does not exist, and then make sure... |
| cumJaccardIndex | Cumulative Jaccard Index |
| cumOverlapCoefficient | Cumulative overlap coefficient |
| cumsumprop | Proportion of cumulative sum over sum |
| cutInterval | Cut a vector of numbers into interval factors. |
| dfFactor | Get a factor vector for a data.frame |
| dfFactor2Str | Convert factor columns in a data.frame into character strings |
| extname | Get the base and extension(s) of file name(s) |
| fixWidthStr | Shorten strings to strings with a fix width of characters |
| getDefaultFontFamily | Get default font family |
| haltifnot | Ensure the Truth of R Expressions and Print Defined Error... |
| headhead | head/tail function for matrix or data.frame |
| headtail | Print head and tail elements of a vector |
| identicalMatrix | Test whether two matrices are identical by values and by dim... |
| identicalMatrixValue | Test whether two matrices have the same numerica values given... |
| imatch | Case-insensitive match and pmatch |
| isDir | Checks existing directory |
| isError | Tell whether an object is an error |
| isRocheCompoundID | Tell whether a character string is a Roche compound ID |
| jaccardIndex | Calculate the Jaccard Index between two vectors |
| keepMaxStatRow | KEEP ROWS WITH THE MAXIMUM STATISTIC |
| libordie | Load a library mutedly and quit (die) in case of failing |
| list2df | Transform a list of character strings into a data.frame |
| listOverlapCoefficient | Pairwise overlap coefficient of lists |
| longdf2matrix | Convert a long-format data frame into matrix |
| matchColumn | Match a column in data.frame to a master vector |
| matchColumnName | Match a given vector to column names of a data.frame or... |
| matrix2longdf | Transform a matrix into a long-format data.frame |
| mergeInfreqLevelsByCumsumprop | Merge infrequent levels by setting the threshold of the... |
| midentical | Multiple identical |
| mmatch | Multiple matching |
| munion | Operations for multiple sets |
| na.false | Replace NA with FALSE |
| naivePairwiseDist | Calculate pairwise distances between each pair of items in a... |
| ofactor | Ordered factor |
| openFileDevice | Open a device as a file preparing for plotting in the file |
| overlapCoefficient | Overlap coefficient, also known as Szymkiewicz-Simpson... |
| pAbsLog10Score | Transform p-values to continuous scores with the... |
| pairwiseJaccardIndex | Calculate pairwise Jaccard Indices between each pair of items... |
| pairwiseOverlapDistance | Calculate pairwise overlap coefficients between each pair of... |
| percentage | Print a decimal number in procent format |
| pQnormScore | Transform p-values to continuous scores with the quantile... |
| print.BEDAinfo | Print BEDAinfo object |
| pScore | Transform p-values to continuous scores |
| putColsFirst | Rearrange columns to put some columns to far left |
| pwdecode | Decode password with function implemented with pwencode |
| pwencode | Encode a password |
| qqmsg | Quitely Quit with Messages |
| qsystem | Quietly runs a system command |
| refactorNum | Sort numeric factor levels by values |
| registerLog | The functions 'registerLog' and 'doLog' provide a simple... |
| relevels | Relevel a factor by a named or unnamed vector. |
| relevelsByNamedVec | Relevel a factor by a named vector. |
| relevelsByNotNamedVec | Relevel a factor by a unnamed vector. |
| reload | Reload a package |
| removeColumns | Remove columns |
| removeInvarCol | Remove invariable columns from a data frame or matrix |
| replaceColumnName | Replace column names in data.frame |
| ribiosTempdir | A temporary directory which (1) every machine in the cluster... |
| ribiosTempfile | A temporary file which (1) every machine in the cluster has... |
| ribiosUtils | ribiosUtils |
| rmat | Remove temporary files at a specified time interval from now |
| rocheCore | Extract core identifiers from Roche compound IDs |
| rowscale | S3 method for row-scaling |
| rowscale.matrix | Scale a matrix by row |
| rsetdiff | Reverse setdiff |
| scriptInit | Prepare R for an interactive script |
| setDebug | Functions for command-line Rscript debugging |
| shortenStr | Shorten strings to a given number of characters |
| silencio | Keep silent by suppressing warnings and messages |
| sortAndFilterByCumsumprop | Sort a numeric vector and filter by a threshold of cumsumprop |
| sortByCol | Sort data.frame rows by values in specified columns |
| sortByDimnames | Sort matrix by dim names |
| strtoken | Tokenize strings by character |
| stubborngc | Repeat garbage-collecting until all resource is freed |
| subsetByColumnName | Subset a data.frame by column name, allowing differences in... |
| summarizeRows | Summarizing rows/columns by a factor |
| trim | Trim leading and tailing spaces from string |
| uniqueLength | Length of unique elements in a vector |
| uniqueNonNA | Make a vector free of NA and unique |
| verbose | Print messages conditional on the verbose level |
| whoami | System user name |
| writeLog | Write text as log to a connection |
