R: Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library

# Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library

## Documentation for package ‘ribiosUtils’ version 1.7.7

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F H I J K L M N O P Q R S T U V W

## -- A --

allIdentical | Testing whether several objects are all identical with each other
apply1 | Summarizing rows/columns by a factor
apply2 | Summarizing rows/columns by a factor
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
assertDir | Checks existing directory
assertFile | Check whether file(s) exist
atofMatrix | Convert string-valued data frame or matrix into a numeric matrix

## -- B --

basefilename | Get the base and extension(s) of file name(s)
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.
boundNorm | Set boundaries for numeric values, or perform a 0-1 normalization.

## -- C --

cbindByRownames | Column bind by rownames
checkDir | Checks existing directory
checkFile | Check whether file(s) exist
chosenFew | Print the chosen few items of a long vector
clearLog | The functions 'registerLog' and 'doLog' provide a simple mechanism to handle loggings (printing text messages to files or other types of connections) in R.
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.
cumJaccardDistance | Cumulative Jaccard Index
cumJaccardIndex | Cumulative Jaccard Index
cumOverlapCoefficient | Cumulative overlap coefficient
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

## -- D --

dfFactor | Get a factor vector for a data.frame
dfFactor2Str | Convert factor columns in a data.frame into character strings
doLog | Write text as log to a connection

## -- E --

equateWellLabelWidth | Format labels for wells in microwell plates to equal widths
extname | Get the base and extension(s) of file name(s)

## -- F --

firstUp | Make the first alphabet of strings uppercase
fixWidthStr | Shorten strings to strings with a fix width of characters
flushLog | The functions 'registerLog' and 'doLog' provide a simple mechanism to handle loggings (printing text messages to files or other types of connections) in R.

## -- H --

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

## -- I --

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
imatchv | Case-insensitive match and pmatch
invertList | Invert the names and elements of a list
ipmatch | Case-insensitive match and pmatch
ipmatchv | Case-insensitive match and pmatch
isDebugging | Functions for command-line Rscript debugging
isDir | Checks existing directory
isError | Tell whether an object is an error
isEven | Whether an integer is odd (or even)
isIntDebugging | Functions for command-line Rscript debugging
isInvarCol | Remove invariable columns from a data frame or matrix
isMaxStatRow | KEEP ROWS WITH THE MAXIMUM STATISTIC
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
isVarCol | Remove invariable columns from a data frame or matrix

## -- J --

jaccardDistance | Calculate the Jaccard Index between two vectors
jaccardIndex | Calculate the Jaccard Index between two vectors

## -- K --

keepMaxStatRow | KEEP ROWS WITH THE MAXIMUM STATISTIC
keepMaxStatRowInd | KEEP ROWS WITH THE MAXIMUM STATISTIC

## -- L --

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

## -- M --

matchColumn | Match a column in data.frame to a master vector
matchColumnIndex | Match a column in data.frame to a master vector
matchColumnName | Match a given vector to column names of a data.frame or matrix
matchv | Case-insensitive match and pmatch
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
mintersect | Operations for multiple sets
mmatch | Multiple matching
mset | Operations for multiple sets
msetdiff | Operations for multiple sets
munion | Operations for multiple sets

## -- N --

na.false | Replace NA with FALSE
naivePairwiseDist | Calculate pairwise distances between each pair of items in a list
nField | Count tokens by splitting strings

## -- O --

ofactor | Ordered factor
orderCutgroup | Reorder the groups by their group size
overlapCoefficient | Overlap coefficient, also known as Szymkiewicz-Simpson coefficient
overlapDistance | Overlap coefficient, also known as Szymkiewicz-Simpson coefficient
overwriteDir | Overwrite a directory

## -- P --

pAbsLog10Score | Transform p-values to continuous scores with the absolute-log10 transformation
pairwiseJaccardDistance | Calculate pairwise Jaccard Indices between each pair of items in a list
pairwiseJaccardIndex | Calculate pairwise Jaccard Indices between each pair of items in a list
pairwiseOverlapCoefficient | Calculate pairwise overlap coefficients 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
pQnormScore | Transform p-values to continuous scores with the quantile function of the normal distribution
print.BEDAinfo | Print BEDAinfo object
pScore | Transform p-values to continuous scores
putColsFirst | Rearrange columns to put some columns to far left
pwdecode | Decode password with function implemented with pwencode
pwencode | Encode a password

## -- Q --

qqmsg | Quitely Quit with Messages
qsystem | Quietly runs a system command

## -- R --

rbindByColnames | Column bind by rownames
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
removeRowsByFunc | Remove rows or column by function
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.default | 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

## -- S --

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
stringDataFrame2numericMatrix | Convert string-valued data frame or matrix into a numeric matrix
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
summarizeCols | Summarizing rows/columns by a factor
summarizeColumns | Summarizing rows/columns by a factor
summarizeRows | Summarizing rows/columns by a factor

## -- T --

tailtail | head/tail function for matrix or data.frame
trim | Trim leading and tailing spaces from string

## -- U --

ulen | Length of unique elements in a vector
uniqueLength | Length of unique elements in a vector
uniqueNonNA | Make a vector free of NA and unique
unsetDebug | Functions for command-line Rscript debugging

## -- V --

verbose | Print messages conditional on the verbose level

## -- W --

wellIndex2position | Translate well index numbers to well positions
whoami | System user name
writeLog | Write text as log to a connection