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 1.26.1
Index]