exprs-methods {xps} | R Documentation

## Get/Set Expression Values

### 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)

[Package xps version 1.2.10 Index]