tni.gsea2 {RTN} | R Documentation |
Uses GSEA2 algorithm to compute regulon activity for
TNI-class
objects.
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)
object |
a preprocessed object of class 'TNI' |
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). |
a list with enrichment scores for all samples in the TNI.
Mauro Castro
TNI-class
tna.gsea2
tna.plot.gsea2
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 GSEA2 analysis pipeline EScores <- tni.gsea2(rtni) #parallel version with SNOW package! library(snow) options(cluster=makeCluster(3, "SOCK")) EScores <- tni.gsea2(rtni) stopCluster(getOption("cluster")) ## End(Not run)