intensity-methods {xps} | R Documentation

## Get/Set Data Values

### Description

Get/set data values from/for class `DataTreeSet`.

Usage

`intensity(object)`
`intensity(object, filename = NULL, verbose = FALSE) <- value`

### Arguments

`object` | object of class `DataTreeSet`.
`filename` | `character` vector containing optional ROOT file name.
`verbose` | logical, if `TRUE` print status information.
`value` | `data.frame` containing expression values.

### Details

Get the intensity values from slot `data` or set slot `data` to `value`.

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

Using replacement method `intensity<-` with default settings will not change the data stored in the ROOT data file, and thus will not have any effect on subsequent processing methods. If you really want to use the replacement data for further processing you must supply a new ROOT `filename`. This will export each intensity column of `value` as CEL-file (version 3), which will then be imported into the new ROOT data file `filename`.

Warning: Do not use replacement method `intensity<-` until you really know what you are doing!

Note: The first two columns of replacement `data.frame` `value` must be the (X,Y) coordinates, followed by the intensities whereby the number of intensity columns must be identical to the columns to be replaced.

Note: If you do not want to replace your current object, create first a copy of type `DataTreeSet` by simply writing `newobj <- oldobj`, and use `newobj` for replacement. This is important since `intensity<-` does also update slots `rootfile`, `filedir` and `treenames` when a new `filename` was chosen.

Note: The CEL-files created are fully functional CEL-files (version 3), however some header rows such as GridCornerUL, AlgorithmParameters, and some of the data in DatHeader are placeholders only.

Warning: The CEL-files created WILL REPLACE THE ORIGINAL CEL-files, if they have identical names to the original CEL-files and the original CEL-files are located in the working directory. Thus the original CEL-files should preferable be located in directory `celdir` of function `import.data`.

### Author(s)

Christian Stratowa

### See Also

`validData`

### 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="/"))

    ## get intensity values
    value <- intensity(data.test3)

    ## make a copy of your object if you do not want to replace it
    newdata.test3 <- data.test3

    ## replace slot data with value
    intensity(newdata.test3, "ReplacementData", FALSE) <- value
    str(newdata.test3)

    ## now you can create an ExprTreeSet using the new intensity data
    data.rma <- rma(newdata.test3,"ReplacementRMA",tmpdir="",background="none",normalize=TRUE,verbose=FALSE)
    ## End(Not run)

[Package xps version 1.4.10 Index]