statisticsForPREDAfromEset {PREDA} | R Documentation

## function to compute a statisticsForPREDA object from an ExpressionSet object

### Description

function to compute a statisticsForPREDA object from an ExpressionSet object

### Usage

    # statisticsForPREDAfromEset(.Object, pData_classColumn=NULL,
    # statisticType=NULL, logged=TRUE, referenceGroupLabel=NULL,
    # classVector=NULL, testedTail="both")

    statisticsForPREDAfromEset(.Object, ...)

### Arguments

`.Object` | Object of class ExpressionSet
`...` | See below pData_classColumn: Column from pData(.Object) containig the labels for different samples classes. statisticType: Stastistic for differential expression that is computed on input data. Possible values are "tstatistic", "FC" (Fold Change), "FCmedian" (fold change computed on medians) logged: Logical value (default TRUE) to specify if the input data are logged (Log2). This parameter will influence the computation of statistics. referenceGroupLabel: Specify which class label is used for the reference sample used in computing statistics for differential expression. classVector: If pData_classColumn is NULL then a vector specifying the sample classes is required and can be provided with classVector parameter testedTail: Specify what tail of the distribution will be tested for significantly extreme values in PREDA analysis. Possible values are "both", "upper" or "lower". Default value is "both".

### Details

An object of class ExpressionSet is used as input and gene centered statistics for differential expression are computed on the contained data. The computed statistics are used to build a StatisticsForPREDA object

### Value

An object of class StatisticsForPREDA

### Author(s)

Francesco Ferrari

### See Also

`"StatisticsForPREDA"`

### Examples

      ## Not run:

    require(PREDAsampledata)

    data(ExpressionSetRCC)

    GEstatisticsForPREDA<-statisticsForPREDAfromEset(
    ExpressionSetRCC, statisticType="tstatistic",
    referenceGroupLabel="normal", classVector=sampleinfo[,"Class"])

    ## End(Not run)

[Package PREDA version 1.40.0 Index]