tni.gsea2 {RTN}R Documentation

Compute regulon activity by calling GSEA2 (two-tailed Gene Set Enrichment Analysis) algorithm

Description

Uses GSEA2 algorithm to compute regulon activity for TNI-class objects.

Usage

tni.gsea2(object, minRegulonSize=15, doSizeFilter=FALSE, scale=FALSE, exponent=1, 
tnet="dpi", tfs=NULL, samples=NULL, features=NULL, refsamp=NULL, log=FALSE, 
alternative=c("two.sided", "less", "greater"), targetContribution=FALSE, 
additionalData=FALSE, verbose=TRUE)

Arguments

object

a preprocessed object of class 'TNI' TNI-class.

minRegulonSize

a single integer or numeric value specifying the minimum number of elements in a regulon. Regulons smaller than this number are removed from the analysis.

doSizeFilter

a logical value. If TRUE, negative and positive targets are independently verified by the 'minRegulonSize' argument.

scale

A logical value specifying if expression values should be centered and scaled across samples (when verbose=TRUE) or not (when verbose=FALSE).

exponent

a single integer or numeric value used in weighting phenotypes in GSEA (see 'gseaScores' function at HTSanalyzeR).

tnet

can take values of 'refnet', 'dpi' or 'cdt'. It refers to the version of the regulatory network that will be used for GSEA analysis.

tfs

an optional vector with transcription factor identifiers.

samples

an optional string vector containing the sample names for which will be computed the GSEA2.

features

a string vector containing features for feature selection.

refsamp

an optional string vector containing the names of the reference samples for differential expression calculations. If not provided, then the average of all samples will be used as reference.

log

a logical value. If TRUE, differential expression calculations will be computed in log space.

alternative

a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less".

targetContribution

This argument is used for internal calls. A single logical value specifying to return the contribution of each target in enrichment scores (when verbose=TRUE) or not (when verbose=FALSE).

additionalData

This argument is used for internal calls. A single logical value specifying to return the additional data objects (when verbose=TRUE) or not (when verbose=FALSE).

verbose

a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

Value

a list with enrichment scores for all samples in the TNI.

Author(s)

Mauro Castro

See Also

TNI-class tna.gsea2 tna.plot.gsea2

Examples


data(tniData)

## Not run: 

rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)
rtni <- tni.dpi.filter(rtni)

#run GSEA2 analysis pipeline
EScores <- tni.gsea2(rtni)

#parallel version with SNOW package!
library(snow)
options(cluster=snow::makeCluster(3, "SOCK"))
EScores <- tni.gsea2(rtni)
stopCluster(getOption("cluster"))


## End(Not run)

[Package RTN version 2.8.5 Index]