transformData {clusterExperiment} | R Documentation

## Transform the original data in a ClusterExperiment object

### Description

Provides the transformed data

### Usage

    ## S4 method for signature 'matrixOrHDF5'
    transformData(object, transFun = NULL, isCount = FALSE)

    ## S4 method for signature 'ClusterExperiment'
    transformData(object, whichAssay = 1, ...)

    ## S4 method for signature 'SingleCellExperiment'
    transformData(object, whichAssay = 1, ...)

    ## S4 method for signature 'SummarizedExperiment'
    transformData(object, ...)

### Arguments

`object` | a matrix, SummarizedExperiment, SingleCellExperiment or ClusterExperiment object.
`transFun` | a transformation function to be applied to the data. If the transformation applied to the data creates an error or NA values, then the function will throw an error. If object is of class `ClusterExperiment`, the stored transformation will be used and giving this parameter will result in an error.
`isCount` | if `transFun=NULL`, then `isCount=TRUE` will determine the transformation as defined by `function(x){log2(x+1)}`, and `isCount=FALSE` will give a transformation function `function(x){x}`. Ignored if `transFun=NULL`. If object is of class `ClusterExperiment`, the stored transformation will be used and giving this parameter will result in an error.
`whichAssay` | numeric or character specifying which assay to use. See `assay` for details.
`...` | Values passed on the the 'matrix' method.

### Details

The data matrix defined by `assay(x)` is transformed based on the transformation function either defined in x (in the case of a `ClusterExperiment` object) or by user given values for other classes.

### Value

A DataFrame defined by `assay(x)` suitably transformed

### Examples

    mat <- matrix(data=rnorm(200), ncol=10)
    mat[1,1] <- -1 #force a negative value
    labels <- gl(5, 2)
    cc <- ClusterExperiment(mat, as.numeric(labels), transformation =
    function(x){x^2}) #define transformation as x^2
    z<-transformData(cc)

[Package clusterExperiment version 2.12.0 Index]