writeQubicInputFile {rqubic} | R Documentation |
The QUBIC commmand line tool (developed by Ma et al.) requires a tab-limited data matrix as input file, with some special requirements (see details below). This function takes an object of ExpressionSet and outputs the file.
writeQubicInputFile(x, file = "", featureNames, sampleNames)
x |
An object inheriting the |
file |
Filename to output, or a connection to write to (e.g. |
featureNames |
Specifies the feature names. It can be left blank,
in which case the result of calling |
sampleNames |
Specifies the sample names. It can be left blank,
in which case the result of calling |
The description of the data
format can be checked by running the QUBIC tool in the command line
mode, with the option -h (for help). A special
requirement, which makes it different from the results of the
write.table
function in R, is that before the sample
names (column names), an “o” must be added.
No visible value will be returned, the function is called for its side effect.
Jitao David Zhang <jitao_david.zhang@roche.com>
tmpfile <- tempfile() data(sample.ExpressionSet, package="Biobase") sub.eset <- sample.ExpressionSet[1:3, 1:3] ## write to standard output writeQubicInputFile(sub.eset) ## write to a temporary file writeQubicInputFile(sub.eset, tmpfile) head(readLines(tmpfile)) ## specify names with one column name in fData/pData writeQubicInputFile(sub.eset, file="", sampleNames="sex") ## alternatively specifiy names manually writeQubicInputFile(sub.eset, file="",sampleNames=paste("Sample", 1:3))