exprs-methods: Get/Set Expression Values

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

Description

Get/set expression values from/for class ExprTreeSet.

Usage

exprs(object)
exprs(object, treenames = NULL) <- value

Arguments

object	object of class ExprTreeSet.
treenames	character vector containing optional tree names to be used as subset.
value	data.frame containing expression values.

Details

Get the expression values from slot data or set slot data to value.

Method exprs returns the expression values from slot data as data.frame, while replacement method exprs<- allows to replace slot data with a data.frame.

In order to create an ExprTreeSet containing only a subset of slot data, first export slot data using method exprs, create a character vector containing only treenames to be used in the subset, and then use replacement method exprs<- to replace slot data with the subset. Slots treenames and numtrees will be updated automatically.

Note: When creating character vector treenames it is sufficient to use the name part of the tree name w/o the extension.

Note: If you do not want to replace your current object, create first a copy of type ExprTreeSet by simply writing newobj <- oldobj, and use newobj for replacement. This is important since exprs<- does also update slots treenames and numtrees as already mentioned.

Author(s)

Christian Stratowa

See Also

pvalData, presCall

Examples

## Not run: 
## 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="/"))

## create an ExprTreeSet
data.rma <- rma(data.test3,"tmp_TestRMA",tmpdir="",background="pmonly",normalize=TRUE,verbose=FALSE)

## get expression values
value <- exprs(data.rma)

## selected treenames only
treenames <- c("TestA2", "TestB1")

## make a copy of your object if you do not want to replace it
subset.rma <- data.rma

## replace slot data with subset
exprs(subset.rma, treenames) <- value
str(subset.rma)

## End(Not run)

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