| Testing whether several objects are all identical with each other | allIdentical |
| Apply isTopOrIncAndNotExcl filter to a matrix | applyTopOrIncAndNotExclFilter |
| Convert string-valued data frame or matrix into a numeric matrix | asNumMatrix atofMatrix stringDataFrame2numericMatrix |
| Assert whether the required column names exist | assertColumnName |
| Check dimensionality of contrast matrix | assertContrast |
| Check dimensionality of design matrix | assertDesign |
| Check dimensionality of both design and contrast matrix | assertDesignContrast |
| Print BEDA project information | bedaInfo |
| Translate BiOmics-Pathology pstore path to URL | biomicsPstorePath2URL |
| Set boundaries for numeric values, or perform a 0-1 normalization. | bound boundNorm |
| Column bind by rownames | cbindByRownames rbindByColnames |
| Check whether file(s) exist | assertFile checkFile |
| Print the chosen few items of a long vector | chosenFew |
| Close connections to all loggers This function closes all open connections set up by loggers It is automatically run at the end of the R session (setup by 'registerLog') | closeLoggerConnections |
| Pairwise jaccard/overlap coefficient can be calculated efficiently using matrix Pairwise overlap coefficient of binary matrix by column | columnOverlapCoefficient |
| Compare two vectors by set operations | compTwoVecs |
| Calculate correlation coefficients using common rows of the two matrices | corByRownames |
| Count tokens by splitting strings | countTokens nField |
| Create a directory if it does not exist, and then make sure the creation was successful. | createDir |
| Copy the skeleton RMarkdown file to a specified location | createRmdTemplate |
| Cumulative Jaccard Index | cumJaccardDistance cumJaccardIndex |
| Cumulative overlap coefficient | cumOverlapCoefficient cumOverlapDistance |
| Proportion of cumulative sum over sum | cumsumprop |
| Cut a vector of numbers into interval factors. | cutInterval |
| Cut a tree into groups of ordered sizes | cutreeIntoOrderedGroups |
| Get a factor vector for a data.frame | dfFactor |
| Convert factor columns in a data.frame into character strings | dfFactor2Str |
| Format labels for wells in microwell plates to equal widths | equateWellLabelWidth |
| Get the base and extension(s) of file name(s) | basefilename extname |
| Make the first alphabet of strings uppercase | firstUp |
| Shorten strings to strings with a fix width of characters | fixWidthStr |
| Ensure the Truth of R Expressions and Print Defined Error Message if NOT | haltifnot |
| head/tail function for matrix or data.frame | headhead tailtail |
| Print head and tail elements of a vector | headtail |
| Test whether two matrices are identical by values and by dim names | identicalMatrix |
| Test whether two matrices have the same numerica values given certain accuracy | identicalMatrixValue |
| Case-insensitive match and pmatch | imatch imatchv ipmatch ipmatchv matchv |
| Invert the names and elements of a list | invertList |
| Checks existing directory | assertDir checkDir isDir |
| Tell whether an object is an error | isError |
| Whether an integer is odd (or even) | isEven isOdd |
| Tell whether a character string is a Roche compound ID | isRocheCompoundID |
| Logical vector of being top or included and not excluded | isTopOrIncAndNotExcl |
| Calculate the Jaccard Index between two vectors | jaccardDistance jaccardIndex |
| KEEP ROWS WITH THE MAXIMUM STATISTIC | isMaxStatRow keepMaxStatRow keepMaxStatRowInd |
| Return last characters from strings | lastChar |
| Load a library mutedly and quit (die) in case of failing | libordie |
| Transform a list of character strings into a data.frame | list2df |
| Pairwise overlap coefficient of lists | listOverlapCoefficient |
| Convert a long-format data frame into matrix | longdf2matrix |
| Match a column in data.frame to a master vector | matchColumn matchColumnIndex |
| Match a given vector to column names of a data.frame or matrix | matchColumnName |
| Transform a matrix into a long-format data.frame | matrix2longdf |
| Merge infrequent levels by setting the threshold of the proportion of cumulative sum over sum a.k.a. cumsumprop | mergeInfreqLevelsByCumsumprop |
| Multiple identical | midentical |
| Multiple matching | mmatch |
| Operations for multiple sets | mintersect mset msetdiff munion |
| Replace NA with FALSE | na.false |
| Calculate pairwise distances between each pair of items in a list | naivePairwiseDist |
| Ordered factor | ofactor |
| Reorder the groups by their group size | orderCutgroup |
| Overlap coefficient, also known as Szymkiewicz-Simpson coefficient | overlapCoefficient overlapDistance |
| Overwrite a directory | overwriteDir |
| Transform p-values to continuous scores with the absolute-log10 transformation | pAbsLog10Score |
| Calculate pairwise Jaccard Indices between each pair of items in a list | pairwiseJaccardDistance pairwiseJaccardIndex |
| Calculate pairwise overlap coefficients between each pair of items in a list | pairwiseOverlapCoefficient pairwiseOverlapDistance |
| Print a decimal number in procent format | percentage |
| Transform p-values to continuous scores with the quantile function of the normal distribution | pQnormScore |
| Print BEDAinfo object | print.BEDAinfo |
| Transform p-values to continuous scores | pScore |
| Rearrange columns to put some columns to far left | putColsFirst |
| Decode password with function implemented with pwencode | pwdecode |
| Encode a password | pwencode |
| Quitely Quit with Messages | qqmsg |
| Quietly runs a system command | qsystem |
| Sort numeric factor levels by values | refactorNum |
| The functions 'registerLog' and 'doLog' provide a simple mechanism to handle loggings (printing text messages to files or other types of connections) in R. | clearLog flushLog registerLog |
| Relevel a factor by a named or unnamed vector. | relevels |
| Relevel a factor by a named vector. | relevelsByNamedVec |
| Relevel a factor by a unnamed vector. | relevelsByNotNamedVec |
| Reload a package | reload |
| Remove columns | removeColumns |
| Remove rows or column by function | removeColumnsByFunc removeRowsByFunc |
| Remove columns in a matrix that contains one or more NAs | removeColumnsWithNA |
| Remove invariable columns from a data frame or matrix | isInvarCol isVarCol removeInvarCol |
| Remove rows in a matrix that contains one or more NAs | removeRowsWithNA |
| Replace column names in data.frame | replaceColumnName |
| Replace p-values of zero | replaceZeroPvalue |
| A temporary directory which (1) every machine in the cluster has access to and (2) has sufficient space | ribiosTempdir |
| A temporary file which (1) every machine in the cluster has access to and (2) there is sufficient space | ribiosTempfile |
| ribiosUtils | ribiosUtils |
| Remove temporary files at a specified time interval from now | rmat |
| Extract core identifiers from Roche compound IDs | rocheCore |
| S3 method for row-scaling | rowscale |
| Scale a matrix by row | rowscale.matrix |
| Scale a table by row | rowscale.table |
| Reverse rank order | rrank rrank.default |
| Get reverse rank orders in each column | rrank.matrix |
| Return a matrix that highlights reverse rank orders of features of interest by column | rrankInd |
| Reverse setdiff | rsetdiff |
| Prepare R for an interactive script | scriptInit |
| Functions for command-line Rscript debugging | isDebugging isIntDebugging setDebug unsetDebug |
| Shorten Roche compounds identifiers | shortenRocheCompoundID |
| Shorten strings to a given number of characters | shortenStr |
| Keep silent by suppressing warnings and messages | silencio |
| Sort a numeric vector and filter by a threshold of cumsumprop | sortAndFilterByCumsumprop |
| Sort data.frame rows by values in specified columns | sortByCol |
| Sort matrix by dim names | sortByDimnames |
| Tokenize strings by character | strtoken |
| Repeat garbage-collecting until all resource is freed | stubborngc |
| Subset a data.frame by column name, allowing differences in cases | subsetByColumnName |
| Summarizing rows/columns by a factor | apply1 apply2 summarizeCols summarizeColumns summarizeRows |
| Trim leading and tailing spaces from string | trim |
| Length of unique elements in a vector | ulen uniqueLength |
| Make a vector free of NA and unique | uniqueNonNA |
| Print messages conditional on the verbose level | verbose |
| Translate well index numbers to well positions | wellIndex2position |
| System user name | whoami |
| Write text as log to a connection | doLog writeLog |
