All functions 


Testing whether several objects are all identical with each other 

Apply isTopOrIncAndNotExcl filter to a matrix 

Convert stringvalued data frame or matrix into a numeric matrix 

Assert whether the required column names exist 

Check dimensionality of contrast matrix 

Check dimensionality of design matrix 

Check dimensionality of both design and contrast matrix 

Print BEDA project information 

Translate BiOmicsPathology pstore path to URL 

Set boundaries for numeric values, or perform a 01 normalization. 

Column bind by rownames 

Check whether file(s) exist 

Print the chosen few items of a long vector 

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 

Pairwise jaccard/overlap coefficient can be calculated efficiently using matrix Pairwise overlap coefficient of binary matrix by column 

Compare two vectors by set operations 

Calculate correlation coefficients using common rows of the two matrices 

Count tokens by splitting strings 

Create a directory if it does not exist, and then make sure the creation was successful. 

Cumulative Jaccard Index 

Cumulative overlap coefficient 

Proportion of cumulative sum over sum 

Cut a vector of numbers into interval factors. 

Cut a tree into groups of ordered sizes 

Get a factor vector for a data.frame 

Convert factor columns in a data.frame into character strings 

Format labels for wells in microwell plates to equal widths 

Get the base and extension(s) of file name(s) 

Make the first alphabet of strings uppercase 

Shorten strings to strings with a fix width of characters 

Ensure the Truth of R Expressions and Print Defined Error Message if NOT 

head/tail function for matrix or data.frame 

Print head and tail elements of a vector 

Test whether two matrices are identical by values and by dim names 

Test whether two matrices have the same numerica values given certain accuracy 

Caseinsensitive match and pmatch 

Invert the names and elements of a list 

Checks existing directory 

Tell whether an object is an error 

Whether an integer is odd (or even) 

Tell whether a character string is a Roche compound ID 

Logical vector of being top or included and not excluded 

Calculate the Jaccard Index between two vectors 

KEEP ROWS WITH THE MAXIMUM STATISTIC 

Return last characters from strings 

Load a library mutedly and quit (die) in case of failing 

Transform a list of character strings into a data.frame 

Pairwise overlap coefficient of lists 

Convert a longformat data frame into matrix 

Match a column in data.frame to a master vector 

Match a given vector to column names of a data.frame or matrix 

Transform a matrix into a longformat data.frame 

Merge infrequent levels by setting the threshold of the proportion of cumulative sum over sum a.k.a. cumsumprop 

Multiple identical 

Multiple matching 

Operations for multiple sets 

Replace NA with FALSE 

Calculate pairwise distances between each pair of items in a list 

Ordered factor 

Reorder the groups by their group size 

Overlap coefficient, also known as SzymkiewiczSimpson coefficient 

Overwrite a directory 

Transform pvalues to continuous scores with the absolutelog10 transformation 

Transform pvalues to continuous scores with the quantile function of the normal distribution 

Transform pvalues to continuous scores 

Calculate pairwise Jaccard Indices between each pair of items in a list 

Calculate pairwise overlap coefficients between each pair of items in a list 

Print a decimal number in procent format 

Print BEDAinfo object 

Rearrange columns to put some columns to far left 

Decode password with function implemented with pwencode 

Encode a password 

Quitely Quit with Messages 

Quietly runs a system command 

Sort numeric factor levels by values 

The functions 

Relevel a factor by a named or unnamed vector. 

Relevel a factor by a named vector. 

Relevel a factor by a unnamed vector. 

Reload a package 

Remove columns 

Remove rows or column by function 

Remove columns in a matrix that contains one or more NAs 

Remove invariable columns from a data frame or matrix 

Remove rows in a matrix that contains one or more NAs 

Replace column names in data.frame 

Replace pvalues of zero 

A temporary directory which (1) every machine in the cluster has access to and (2) has sufficient space 

A temporary file which (1) every machine in the cluster has access to and (2) there is sufficient space 

ribiosUtils 

Remove temporary files at a specified time interval from now 

Extract core identifiers from Roche compound IDs 

S3 method for rowscaling 

Scale a matrix by row 

Scale a table by row 

Reverse rank order 

Get reverse rank orders in each column 

Return a matrix that highlights reverse rank orders of features of interest by column 

Reverse setdiff 

Prepare R for an interactive script 

Functions for commandline Rscript debugging 

Shorten Roche compounds identifiers 

Shorten strings to a given number of characters 

Keep silent by suppressing warnings and messages 

Sort a numeric vector and filter by a threshold of cumsumprop 

Sort data.frame rows by values in specified columns 

Sort matrix by dim names 

Tokenize strings by character 

Repeat garbagecollecting until all resource is freed 

Subset a data.frame by column name, allowing differences in cases 

Summarizing rows/columns by a factor 

Trim leading and tailing spaces from string 

Length of unique elements in a vector 

Make a vector free of NA and unique 

Print messages conditional on the verbose level 

Translate well index numbers to well positions 

System user name 

Write text as log to a connection 