Package index • 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