tna.gsea1: One-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 the results of the GSEA analysis over a list of regulons in a transcriptional network (with multiple hypothesis testing corrections).

Usage

tna.gsea1(object, pValueCutoff=0.05, pAdjustMethod="BH",  minRegulonSize=15, 
sizeFilterMethod="posORneg", nPermutations=1000, exponent=1, tnet="dpi", 
orderAbsValue=TRUE, tfs=NULL, verbose=TRUE)

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".
orderAbsValue	a single logical value indicating whether the values should be converted to absolute values and then ordered (if TRUE), or ordered as they are (if FALSE).
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).

Value

a data frame in the slot "results", see 'gsea1' option in tna.get.

Author(s)

Mauro Castro, Xin Wang

See Also

TNA-class tna.plot.gsea1

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 GSEA1 analysis pipeline
rtna <- tna.gsea1(rtna)

#get results
tna.get(rtna, what="gsea1")

# run parallel version with SNOW package!
library(snow)
options(cluster=snow::makeCluster(3, "SOCK"))
rtna <- tna.gsea1(rtna)
stopCluster(getOption("cluster"))

## End(Not run)

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