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

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Documentation for package ‘ribiosUtils’ version 1.5-6

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A B C D E F G 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
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

-- C --

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.
closeFileDevice Open a device as a file preparing for plotting in the file
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
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.

-- 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 --

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

-- F --

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.

-- G --

getDefaultFontFamily Get default font family

-- 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
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
isIntDebugging Functions for command-line Rscript debugging
isInvarCol Remove invariable columns from a data frame or matrix
isMaxStatRow KEEP ROWS WITH THE MAXIMUM STATISTIC
isRocheCompoundID Tell whether a character string is a Roche compound ID
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 --

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
openFileDevice Open a device as a file preparing for plotting in the file
overlapCoefficient Overlap coefficient, also known as Szymkiewicz-Simpson coefficient
overlapDistance Overlap coefficient, also known as Szymkiewicz-Simpson coefficient

-- 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 --

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
removeInvarCol Remove invariable columns from a data frame or matrix
replaceColumnName Replace column names in data.frame
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
rsetdiff Reverse setdiff

-- S --

scriptInit Prepare R for an interactive script
setDebug Functions for command-line Rscript debugging
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 --

whoami System user name
writeLog Write text as log to a connection