writeToFile {arrayMagic} | R Documentation |
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 [] ).
writeToFile(arrayDataObject, exprSetRGObject, additionalDataMatrix, rowSelection, slideNameColumn, channels=c("logRatio"), fileName="dumpedData.txt", savePath=".", fullOutput=TRUE, coding=FALSE)
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", "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 |
The function is called for its side effect, i.e. writing a file.
Andreas Buness <a.buness@dkfz.de>
exprSetRG-class
,
arrayData-class
,
write.htmltable