writeToFile {arrayMagic}R Documentation

Writes a textual representation of an exprSetRG and/or arrayData object

Description

writeToFile generates a well-formated tab-deliminated output file of data stored in the exprSetRG and/or arrayData objects. Different "views" on either a corresponding pair of an exprSetRG- and an arrayData-object or of a single object itself are possible. The argument channels allows to specify the "views". The microarray slide or channel annotation, as well as the spot annotation is aligned to the data block if given. For further restriction and control of the output, e.g. slide subsets or ordering of slides, you may use the subsetting operations offered by the exprSetRG-class and arrayData-class beforehand (e.g. slideSubset and [] ).

Usage

writeToFile(arrayDataObject, exprSetRGObject, additionalDataMatrix, rowSelection, slideNameColumn, channels=c("logRatio"), fileName="dumpedData.txt", savePath=".", fullOutput=TRUE, coding=FALSE)

Arguments

arrayDataObject object of class arrayData; optional/required, cf. channels; default: missing
exprSetRGObject object of class exprSetRG; optional/required, cf. channels; default: missing
additionalDataMatrix class matrix; optional; default: missing. The rows must correspond to those of the data objects; colnames must be supplied.
rowSelection vector of indexes; optional; default: missing
slideNameColumn character string; optional; default: missing; must refer to a valid column in getHybAttr(arrayDataObject) or in pDataSlide(exprSetRGobject)
channels vector of character strings; default: c("logRatio"); valid character strings are: "logRatio", "green", "red", "greenRelative", "redRelative", "rawGreen", "rawRed", "rawGreenRelative", "rawRedRelative", "se.exprsLogRatio", "se.exprsGreen", "se.exprsRed". "Raw"-types must not mix with not "raw"-types and vice versa. "logRatio"-types must not mix with "colour"-types. The "raw" types require the argument arrayDataObject, all other types requires at least the argument exprSetRGObject.
fileName character string; required; default: "dumpedData.txt"
savePath character string; required; default: "."
fullOutput logical; adds phenoData information at the top of the table ; by default: TRUE
coding logical; adds integer-coded-phenoData information at the top to the table only if coding = TRUE and fullOutput = TRUE; default: FALSE

Details

Value

The function is called for its side effect, i.e. writing a file.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

exprSetRG-class, arrayData-class, write.htmltable

Examples

  
 

[Package arrayMagic version 1.8.0 Index]