| export {xps} | R Documentation |
Export data from classes SchemeTreeSet, DataTreeSet,
ExprTreeSet, or CallTreeSet to outfile.
export.scheme(xps.scheme, treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE) export.data(xps.data, treename = "*", treetype = "cel", varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE) export.expr(xps.expr, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE) export.call(xps.call, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE) export(object, ...)
xps.scheme |
an object of type SchemeTreeSet. |
xps.data |
an object of type DataTreeSet. |
xps.expr |
an object of type ExprTreeSet. |
xps.call |
an object of type CallTreeSet. |
treename |
vector of tree names to export. |
treetype |
type of tree(s) to export, see validTreetype |
varlist |
names of tree leaves to export |
outfile |
name of output file. |
sep |
column separator |
as.dataframe |
if TRUE a data.frame will be returned. |
verbose |
logical, if TRUE print status information. |
object |
object of class DataTreeSet. |
... |
arguments treenames,treetype,varlist,outfile,sep,as.dataframe. |
Export data from classes SchemeTreeSet, DataTreeSet,
ExprTreeSet, or CallTreeSet to outfile.
Parameter varlist lists the parameters to export:
- parameters are separated by ":", e.g. varlist="fInten:fStdev".
- for varlist="*" all valid parameters will be exported.
For class DataTreeSet the following varlist parameters are valid:
fInten: | intensities from e.g. tree.cel. | |
fStdev: | standard deviation from e.g. tree.cel. | |
fNPixels: | number of pixels from e.g. tree.cel. | |
fBg: | background values (background trees only). |
For classes ExprTreeSet and CallTreeSet varlist can contain annotation
parameters and parameters of the resulting data.
Following varlist annotation parameters are valid:
fUnitName: | unit name (probeset ID). | |
fTranscriptID: | transcript_id (probeset ID). | |
fName: | gene name. | |
fSymbol: | gene symbol. | |
fAccession: | mRNA accession such as Refseq ID. | |
fEntrezID: | entrez ID. | |
fChromosome: | chromosome. | |
fStart: | start position. | |
fStop: | stop position. | |
fStrand: | strand on chromosome. | |
fCytoBand: | cytoband. |
Following varlist parameters are valid for ExprTreeSet:
fLevel: | expression level. | |
fStdev: | standard deviation. | |
fNPairs: | number of pairs. |
Following varlist parameters are valid for CallTreeSet:
fCall: | detection call. | |
fPValue: | detection p-value. |
An example: varlist="fUnitName:fName:fSymbol:fLevel:fStdev:fEntrezID"
export is a generic method to export data from ROOT trees as text file.
If as.dataframe is TRUE, the data will be imported into the
current R session as data.frame. Otherwise, NULL will be returned.
Christian Stratowa
## load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))
## export as table only
export(scheme.test3, treetype="idx", outfile="Test3_idx.txt",verbose=FALSE)
## export as table and import as data.frame
ann <- export.scheme(scheme.test3, treetype="ann", outfile="Test3_ann.txt",as.dataframe=TRUE,verbose=FALSE)
head(ann)
data <- export.data(data.test3, outfile="Test3_cel.txt",as.dataframe=TRUE,verbose=FALSE)
head(data)