import.data {xps} | R Documentation |
Import the Affymetrix CEL files into a ROOT file and create S4 class DataTreeSet
import.data(xps.scheme, filename = character(0), filedir = getwd(), celdir = NULL, celfiles = "*", celnames = NULL, project = NULL, verbose = TRUE)
xps.scheme |
a SchemeTreeSet containing the correct scheme for the CEL-files |
filename |
file name of ROOT data file. |
filedir |
system directory where ROOT data file should be stored. |
celdir |
system directory containing the CEL-files for corresponding scheme. |
celfiles |
optional vector of CEL-files to be imported. |
celnames |
optional vector of names which should replace the CEL-file names. |
project |
optional class ProjectInfo . |
verbose |
logical, if TRUE print status information. |
import.data
is used to import CEL-files from directory celdir
into
a ROOT
data file. To import only a subset of CEL-files, list these CEL-files
as vector celfiles
.
To import CEL-files from different directories, vector celfiles
must contain the
full path for each CEL-file and celdir
must be celdir=NULL
.
Currently, the following types of Affymetrix CEL-files can be imported: text (version 3), xml, binary (xda), generic (agcc,calvin)
An S4 class DataTreeSet
will be created, serving as R wrapper to the
ROOT
data file filename
.
Use function root.data
to access the ROOT
data file from new
R sessions to avoid creating a new ROOT
data file for every session.
A DataTreeSet
object.
As mentioned above, use function root.data
to access the
ROOT data file from new R sessions to avoid creating a new ROOT
data file
for every R session.
Do not separate filename
of ROOT files with dots, use underscores, e.g. do not use
filename="Data.Test3"
but use filename="Data_Test3"
or filename="DataTest3"
instead.
To every ROOT data file the extension “_cel” is attached to filename
to easily
recognize ROOT data files containing the raw CEL data, e.g. for filename="Data_Test3"
the final name is “Data_Test3_cel.root”. Extension “root” is added automatically,
so that ROOT is able to recognize the file as ROOT file.
Once a ROOT
file is created it can not be overwritten, it must be deleted
manually first. Only ROOT
files called “tmp” or with filename
starting with “tmp_” will be re-created automatically.
If CEL-file names contain dots and/or colons as characters, these characters will be replaced
by underscores. It is recommended to use parameter celnames
to create shorter CEL names
and to replace special characters.
Christian Stratowa
## get scheme and import CEL-files from package scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/")) data.test3 <- import.data(scheme.test3,"tmp_data_test3",celdir=paste(.path.package("xps"),"raw",sep="/")) unlist(treeNames(data.test3)) ## import only subset of CEL-files subdata.test3 <- import.data(scheme.test3,"tmpdt_data_test3",celdir=paste(.path.package("xps"),"raw",sep="/"), celfiles=c("TestA1.CEL","TestB2.CEL"),verbose=FALSE) unlist(treeNames(subdata.test3))