Function reference • ribiosUtils

All functions
`allIdentical()`	Testing whether several objects are all identical with each other
`applyTopOrIncAndNotExclFilter()`	Apply isTopOrIncAndNotExcl filter to a matrix
`asNumMatrix()`	Convert string-valued data frame or matrix into a numeric matrix
`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
`bound()` `boundNorm()`	Set boundaries for numeric values, or perform a 0-1 normalization.
`cbindByRownames()` `rbindByColnames()`	Column bind by rownames
`checkFile()` `assertFile()`	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 open connections set up by loggers It is automatically run at the end of the R session (setup by `registerLog`)
`columnOverlapCoefficient()`	Pairwise jaccard/overlap coefficient can be calculated efficiently using matrix Pairwise overlap coefficient of binary matrix by column
`compTwoVecs()`	Compare two vectors by set operations
`corByRownames()`	Calculate correlation coefficients using common rows of the two matrices
`countTokens()`	Count tokens by splitting strings
`createDir()`	Create a directory if it does not exist, and then make sure the creation was successful.
`cumJaccardIndex()` `cumJaccardDistance()`	Cumulative Jaccard Index
`cumOverlapCoefficient()` `cumOverlapDistance()`	Cumulative overlap coefficient
`cumsumprop()`	Proportion of cumulative sum over sum
`cutInterval()`	Cut a vector of numbers into interval factors.
`cutreeIntoOrderedGroups()`	Cut a tree into groups of ordered sizes
`dfFactor()`	Get a factor vector for a data.frame
`dfFactor2Str()`	Convert factor columns in a data.frame into character strings
`equateWellLabelWidth()`	Format labels for wells in microwell plates to equal widths
`extname()`	Get the base and extension(s) of file name(s)
`firstUp()`	Make the first alphabet of strings uppercase
`fixWidthStr()`	Shorten strings to strings with a fix width of characters
`haltifnot()`	Ensure the Truth of R Expressions and Print Defined Error Message if NOT
`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 names
`identicalMatrixValue()`	Test whether two matrices have the same numerica values given certain accuracy
`imatch()`	Case-insensitive match and pmatch
`invertList()`	Invert the names and elements of a list
`isDir()` `checkDir()` `assertDir()`	Checks existing directory
`isError()`	Tell whether an object is an error
`isOdd()` `isEven()`	Whether an integer is odd (or even)
`isRocheCompoundID()`	Tell whether a character string is a Roche compound ID
`isTopOrIncAndNotExcl()`	Logical vector of being top or included and not excluded
`jaccardIndex()` `jaccardDistance()`	Calculate the Jaccard Index between two vectors
`keepMaxStatRow()`	KEEP ROWS WITH THE MAXIMUM STATISTIC
`lastChar()`	Return last characters from strings
`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 matrix
`matrix2longdf()`	Transform a matrix into a long-format data.frame
`mergeInfreqLevelsByCumsumprop()`	Merge infrequent levels by setting the threshold of the proportion of cumulative sum over sum a.k.a. cumsumprop
`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 list
`ofactor()`	Ordered factor
`orderCutgroup()`	Reorder the groups by their group size
`overlapCoefficient()` `overlapDistance()`	Overlap coefficient, also known as Szymkiewicz-Simpson coefficient
`overwriteDir()`	Overwrite a directory
`pAbsLog10Score()`	Transform p-values to continuous scores with the absolute-log10 transformation
`pQnormScore()`	Transform p-values to continuous scores with the quantile function of the normal distribution
`pScore()`	Transform p-values to continuous scores
`pairwiseJaccardIndex()` `pairwiseJaccardDistance()`	Calculate pairwise Jaccard Indices between each pair of items in a list
`pairwiseOverlapDistance()` `pairwiseOverlapCoefficient()`	Calculate pairwise overlap coefficients between each pair of items in a list
`percentage()`	Print a decimal number in procent format
`print(<BEDAinfo>)`	Print BEDAinfo object
`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 mechanism to handle loggings (printing text messages to files or other types of connections) in R.
`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
`removeColumnsByFunc()` `removeRowsByFunc()`	Remove rows or column by function
`removeColumnsWithNA()`	Remove columns in a matrix that contains one or more NAs
`removeInvarCol()`	Remove invariable columns from a data frame or matrix
`removeRowsWithNA()`	Remove rows in a matrix that contains one or more NAs
`replaceColumnName()`	Replace column names in data.frame
`replaceZeroPvalue()`	Replace p-values of zero
`ribiosTempdir()`	A temporary directory which (1) every machine in the cluster has access to and (2) has sufficient space
`ribiosTempfile()`	A temporary file which (1) every machine in the cluster has access to and (2) there is sufficient space
`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
`rowscale(<table>)`	Scale a table by row
`rrank()`	Reverse rank order
`rrank(<matrix>)`	Get reverse rank orders in each column
`rrankInd()`	Return a matrix that highlights reverse rank orders of features of interest by column
`rsetdiff()`	Reverse setdiff
`scriptInit()`	Prepare R for an interactive script
`setDebug()`	Functions for command-line Rscript debugging
`shortenRocheCompoundID()`	Shorten Roche compounds identifiers
`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 cases
`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
`wellIndex2position()`	Translate well index numbers to well positions
`whoami()`	System user name
`writeLog()`	Write text as log to a connection

Reference

All functions