tna.gsea2: Two-tailed Gene Set Enrichment Analysis (GSEA) over a list of...

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

This function takes a TNA object and returns a CMAP-like analysis obtained by two-tailed GSEA over a list of regulons in a transcriptional network (with multiple hypothesis testing corrections).

Usage

tna.gsea2(object, pValueCutoff=0.05, pAdjustMethod="BH", minRegulonSize=15, 
sizeFilterMethod="posORneg", nPermutations=1000, exponent=1, tnet="dpi", 
tfs=NULL, verbose=TRUE, doSizeFilter=NULL)

Arguments

object	a preprocessed object of class 'TNA' TNA-class.
pValueCutoff	a single numeric value specifying the cutoff for p-values considered significant.
pAdjustMethod	a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details).
minRegulonSize	a single integer or numeric value specifying the minimum number of elements in a regulon that must map to elements of the gene universe. Gene sets with fewer than this number are removed from the analysis.
sizeFilterMethod	a single character value specifying the use of the 'minRegulonSize' argument, which is applyed to regulon's positive and negative targets. Options: "posANDneg", "posORneg", "posPLUSneg". For "posANDneg", the number of both positive and negative targets should be > 'minRegulonSize'; for "posORneg", the number of either positive or negative targets should be > 'minRegulonSize'; and for "posPLUSneg", the number of all targets should be > 'minRegulonSize'.
nPermutations	a single integer or numeric value specifying the number of permutations for deriving p-values in GSEA.
exponent	a single integer or numeric value used in weighting phenotypes in GSEA (see 'gseaScores' function at HTSanalyzeR).
tnet	a single character value specifying which transcriptional network should to used to compute the GSEA analysis. Options: "dpi" and "ref".
tfs	an optional vector with transcription factor identifiers.
verbose	a single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).
doSizeFilter	'doSizeFilter' is deprecated, please use the 'filterSize' parameter.

Value

a data frame in the slot "results", see 'gsea2' option in tna.get.

Author(s)

Mauro Castro

See Also

TNA-class tna.plot.gsea2

Examples

data(tniData)
data(tnaData)

## 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)
rtna <- tni2tna.preprocess(rtni, phenotype=tnaData$phenotype, 
        hits=tnaData$hits, phenoIDs=tnaData$phenoIDs)

#run GSEA2 analysis pipeline
rtna <- tna.gsea2(rtna)

#get results
tna.get(rtna, what="gsea2")

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

## End(Not run)

RTN documentation built on Nov. 12, 2020, 2:02 a.m.