GSCA-class {HTSanalyzeR} | R Documentation |
This S4 class includes a series of methods to do gene set enrichment analysis and hypergeometric tests for high-throughput screens.
Objects of class GSCA
can be created from
new("GSCA", listOfGeneSetCollections, geneList, hits)
(see
the examples below)
listOfGeneSetCollections
:a list of gene set collections (a 'gene set collection' is a list of gene sets).
geneList
:a numeric or integer vector of phenotypes named by gene identifiers.
hits
:a character vector of the gene identifiers (used as hits in the hypergeometric tests).
para
:a list of parameters for hypergeometric tests and GSEA. These
parameters are pValueCutoff
, pAdjustMethod
, nPermutations
,
minGeneSetSize
and exponent
(see function
analyzeGeneSetCollections
for detailed descriptions about
these parameters).
result
:a list of results (see the returned values in the function
analyzeGeneSetCollections
).
summary
:a list of summary information for listOfGeneSetCollections
,
geneList
, hits
, para
, and result
.
preprocessed
:a single logical value specifying whether or not the input data has been preprocessed.
An overview of methods with class-specific functionality: More detailed introduction can be found in help for each specific function.
preprocess
do preprocessing on input vectors of phenotypes and hits including:
a) removing NAs in the geneList
and hits
;
b) invoking function duplicateRemover
to process
duplicated phenotypes (see duplicateRemover
for more details);
c) invoking function annotationConvertor
to convert annotations;
d) ranking phenotypes in a decreasing order.
analyze
perform hypergeometric tests and Gene Set Enrichment Analysis based on
input parameter list para
.
appendGSTerms
append gene set terms to GSCA results
summarize
print summary information about listOfGeneSetCollections
,
geneList
, hits
, para
, and result
.
getTopGeneSets
select top significant gene sets from object@results$`resultName`
by setting ntop
or allSig
.
writeHits
write observed hits in gene sets for hypergeometric tests.
viewGSEA
view a figure of GSEA results for a gene set in a gene set collection.
plotGSEA
plot and save figures of GSEA results for top significant gene sets in a gene set collection.
viewEnrichMap
plot an enrichment map for GSEA or hypergeometric test results
plotEnrichMap
plot and save an enrichment map for GSEA or hypergeometric test results
report
generate html reports.
Xin Wang xw264@cam.ac.uk
preprocess
analyze
appendGSTerms
summarize
getTopGeneSets
writeHits
viewGSEA
plotGSEA
viewEnrichMap
plotEnrichMap
report
## Not run: library(org.Dm.eg.db) library(KEGG.db) library(AnnotationDbi) ##library(igraph) ##load data for enrichment analyses data("KcViab_Data4Enrich") ##select hits hits <- names(KcViab_Data4Enrich)[which(abs(KcViab_Data4Enrich) > 2)] ##set up a list of gene set collections PW_KEGG <- KeggGeneSets(species = "Dm") gscs <- list(PW_KEGG = PW_KEGG) ##create an object of class 'GSCA' gsca <- new("GSCA", listOfGeneSetCollections=gscs, geneList = KcViab_Data4Enrich, hits = hits) ##do preprocessing (KcViab_Data4Enrich has already been preprocessed) gsca <- preprocess(gsca, species="Dm", initialIDs = "Entrez.gene", keepMultipleMappings = TRUE, duplicateRemoverMethod = "max", orderAbsValue = FALSE) ##do hypergeometric tests and GSEA gsca <- analyze(gsca, para = list(pValueCutoff = 0.05, pAdjustMethod = "BH", nPermutations = 1000, minGeneSetSize = 60, exponent = 1)) ##print summary information summarize(gsca) ##get all significant gene sets in "PW_KEGG" sigGSs<-getTopGeneSets(gsca, "GSEA.results", "PW_KEGG", allSig=TRUE) ##view a GSEA figure viewGSEA(gsca, gscName="PW_KEGG", gsName=sigGSs[["PW_KEGG"]][1]) dev.off() ##append gene set terms to results gsca<-appendGSTerms(gsca, keggGSCs="PW_KEGG") ##view an enrichment map for GSEA results eb<-viewEnrichMap(gsca, gscs="PW_KEGG", allSig=TRUE, gsNameType="term", displayEdgeLabel=FALSE, layout="layout.fruchterman.reingold") ##write html reports report(object = gsca, experimentName = "GSCATest", species = "Dm", allSig = TRUE, keggGSCs = "PW_KEGG", reportDir="GSCATestReport") ##browse the index page browseURL(file.path(getwd(), "GSCATestReport", "index.html")) ## End(Not run)