| exprs-methods {xps} | R Documentation |
Get/set expression values from/for class ExprTreeSet.
Usage
exprs(object)
exprs(object, treenames = NULL) <- value
object |
object of class ExprTreeSet. |
treenames |
character vector containing optional tree names to be used as subset. |
value |
data.frame containing expression values. |
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.
Christian Stratowa
## 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)