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                   Set boundaries for numeric values, or perform a
                        0-1 normalization.
cbindByRownames         Column bind by rownames
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 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         Cumulative Jaccard Index
cumOverlapCoefficient   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                   Checks existing directory
isError                 Tell whether an object is an error
isOdd                   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            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      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    Calculate pairwise Jaccard Indices between each
                        pair of items in a list
pairwiseOverlapDistance
                        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     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
