Compute pairwise distances between sample according to their (Prototype Ranked List) PRL, a N x N distance matrix is generated by calling this function, N is the length of PRL.
1 
MergingSet 
an ExpressionSet object. The assay data represents the PRLs of the samples, each column represents one PRL. The number of sample of this argument must be greater than 1, otherwise, this function is not meaningful. 
SignatureLength 
the length of "gene signature". In order to compute pairwise distances among samples, genes lists are ranked according to the gene expression ratio (fold change). And the "gene signature" includes the most upregulated genes (near the top of the list) and the most downregulated genes (near the bottom of the list). 
ScoringDistance 
the distance measurements between PRLs: the Average Enrichment Score Distance (avg), and the Maximum Enrichment Score Distance (max). 
p.value 
logical, if TRUE return a matrix of p.values of the distance matrix, default FALSE 
Once the PRL obtained for each sample, the distances between samples are calculated base on gene signature, including the expression of genes that seemed to consistently vary in response to the across different experimental conditions (e.g., different cell lines and different dosages). We take two distance measurements between PRLs: the Average EnrichmentScore Distance Davg=(TESx,y+TESy,x)/2, and the Maximum EnrichmentScore Distance Dmax=Min(TESx,y,TESy,x)/2.The avg is more stringent than max, where max is more sensitive to weak similarities, with lower precision but large recall.
an distancematrix, the max distance is more sensitive to weak similarities, providing a lower precision but a larger recall.
If p.value is set to TRUE, then a list is returned that consists of the distance matrix as well as their p.values, otherwise, without p.vlues in the result.
ScorePGSEA
, SignatureDistance
1 2 3 4 5 6 7 8  # load the sample expressionSet
data(exampleSet)
# Merging each group of the ranked lists in the exampleSet with the same phenotypic data into a single PRL
MergingSet=RankMerging(exampleSet,"Spearman")
# get the distance matrix
ds=ScoreGSEA(MergingSet,250,"avg")

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
All documentation is copyright its authors; we didn't write any of that.