NWA-class {HTSanalyzeR} | R Documentation |
This class includes a series of methods to do network analysis for high-throughput screens.
Objects of class NWA
can be created from
new("NWA", pvalues, phenotypes=NULL, interactome=NULL)
(see
the examples below)
pvalues
:a numeric vector of p-values.
phenotypes
:a numeric or integer vector of phenotypes.
interactome
:an object of class graphNEL
.
fdr
:one parameter for BioNet to score nodes in the interactome.
result
:a list consisting of subnetwork module identified by BioNet and a vector of labels for nodes of the subnetwork module.
summary
:a list of summary information for p-values
, phenotypes
,
interactome
and result
.
preprocessed
:a logical value specifying whether or not 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 for the input vector of p-values and the vector
of phenotypes including:
a) removing NAs in p-values
and phenotypes
;
b) invoking function duplicateRemover
to process
duplicated phenotypes and p-values (see duplicateRemover
for more details);
c) invoking function annotationConvertor
to convert
annotations;
analyze
invoke function networkAnalysis
to identify enriched sub-
networks based on input parameter list para
.
summarize
print summary information about p-values
, phenotypes
,
interactome
and result
.
interactome
build an interactome for the network analysis.
viewSubNet
plot a figure of identified subnetwork.
plotSubNet
plot and save a figure of identified subnetwork.
report
generate html reports.
Xin Wang xw264@cam.ac.uk
preprocess
analyze
summarize
interactome
viewSubNet
plotSubNet
report
## Not run: library(BioNet) ##load p-values and phenotypes data("KcViab_PVals","KcViab_Data4Enrich") ##load Biogrid interactome for Drosophila Melanogaster data("Biogrid_DM_Interactome") ##create a NWA (NetWork Analysis) object nwa <- new("NWA", pvalues=KcViab_PVals, phenotypes=KcViab_Data4Enrich, interactome=Biogrid_DM_Interactome) ##preprocessing nwa <- preprocess(nwa, species="Dm", initialIDs="Entrez.gene", keepMultipleMappings=TRUE, duplicateRemoverMethod="max") ##To create an interactome nwa <- interactome(nwa, species="Dm", reportDir="HTSanalyzerReport", genetic=FALSE) ##do network analysis nwa <- analyze(nwa, fdr=0.001, species="Dm") graphics.off() ##view identified subnetwork viewSubNet(nwa) ##report to html pages report(object=nwa, experimentName="NWATest", species="Dm", allSig=TRUE, keggGSCs="PW_KEGG", goGSCs=c("GO_BP", "GO_MF", "GO_CC"), reportDir= "NWATestReport") ##browse the index page of the report browseURL(file.path(getwd(), "NWATestReport", "index.html")) ## End(Not run)