tni.area3 {RTN}R Documentation

Compute regulon activity by calling aREA (analytic Rank-based Enrichment Analysis) algorithm

Description

Uses aREA 3-tail algorithm to compute regulon activity for TNI-class objects.

Usage

tni.area3(object, minRegulonSize=15, doSizeFilter=FALSE, scale=FALSE, tnet="dpi", 
tfs=NULL, samples=NULL, features=NULL, refsamp=NULL, log=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).

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 regulon activity.

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.

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.

References

Alvarez et al. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nature Genetics, 48(8):838-847, 2016.

See Also

TNI-class aREA

Examples


data(dt4rtn)

# select 5 regulatoryElements for a quick demonstration!
tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")]

## Not run: 

rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test, 
        rowAnnotation=dt4rtn$gexpIDs)
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)
rtni <- tni.dpi.filter(rtni)

#run aREA algorithm
EScores <- tni.area3(rtni)


## End(Not run)

[Package RTN version 2.6.3 Index]