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)