root.expr: Create class ExprTreeSet accessing ROOT expression file

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Create class ExprTreeSet accessing ROOT expression file.

Usage

root.expr(xps.scheme, rootfile = character(0), treetype = character(0), treenames = "*")

Arguments

xps.scheme	A SchemeTreeSet containing the correct scheme for the ROOT data file.
rootfile	name of ROOT data file, including full path.
treetype	tree type.
treenames	optional character vector of tree names to get only subset of trees.

Details

An S4 class ExprTreeSet will be created, serving as R wrapper to the existing ROOT expression file rootfile.

Parameter treetype must be supplied to identify the ROOT trees for slot data. Valid tree types are listed in validTreetype.

To get the names of all trees with their extensions treetype, which are stored in rootfile, you can call function getTreeNames first.

If the ExprTreeSet should only handle a subset of the trees stored in rootfile, the tree names must be supplied as vector treenames.

Value

A ExprTreeSet object.

Author(s)

Christian Stratowa

See Also

root.data, root.call

Examples

## first, load 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="/"))

# rma
all.rma <- rma(data.test3,"tmp_Test3RMAAll",tmpdir="",background="pmonly",normalize=TRUE,verbose=FALSE)

## use subset of trees
sub.rma <- root.expr(scheme.test3, "tmp_Test3RMAAll.root", "mdp", c("TestA2.mdp", "TestB1"))

xps documentation built on Nov. 8, 2020, 6 p.m.