| CondSEA {gep2pep} | R Documentation |
Condition Set Enrichment Analysis (CondSEA) can be seen as a Gene-SEA performed over rows (as opposed to columns) of a matrix of GEPs. It tells how much a pathway is consistently dysregulated under a set of conditions (such as a set of drug treatments, disease states, cell types, etc.) when compared to a statistical background of other conditions.
CondSEA(rp_peps, pgset, bgset = "all", collections = "all", details = TRUE)
rp_peps |
A repository created with
|
pgset |
A vector of names of conditions. Corresponding PEPs
must exist in all the pathway collections currently in
|
bgset |
The background against which to compare
|
collections |
A subset of the collection names returned by
|
details |
If TRUE (default) rank details will be reported for
each condition in |
For each pathway, all conditions are ranked by how much
they dysregulate it (from the most UP-regulating to the most
DOWN-regulating). Then, a Kolmogorov-Smirnov (KS) test is
performed to compare the ranks assigned to conditions in
pgset against the ranks assigned to conditions in
bgset. A positive (negative) Enrichment Score (ES) of
the KS test indicates whether each pathway is UP- (DOWN-)
regulated by pgset as compared to bgset. A
p-value is associated to the ES.
When PEPs are obtained from drug-induced gene expression
profiles, PathSEA can be used to perform Drug-Set
Enrichment Analysis [1].
A list of 2, by names "CondSEA" and "details". The
"CondSEA" entry is a 2-columns matrix including ESs and
p-values (see details) for each pathway database and
condition. The "details" entry reports the rank of each
condition in pgset for each pathway.
[1] Napolitano F. et al, Drug-set enrichment analysis: a novel tool to investigate drug mode of action. Bioinformatics 32, 235-241 (2016).
getResults, getDetails
db <- loadSamplePWS()
db <- as.CategorizedCollection(db)
repo_path <- file.path(tempdir(), "gep2pepTemp")
rp <- createRepository(repo_path, db)
geps <- loadSampleGEP()
buildPEPs(rp, geps)
pgset <- c("(+)_chelidonine", "(+/_)_catechin")
psea <- CondSEA(rp, pgset)
getResults(psea, "c3_TFT")
unlink(repo_path, TRUE)