NWA-class: An S4 class for NetWork Analysis on high-throughput screens

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description

This class includes a series of methods to do network analysis for high-throughput screens.

Objects from the Class

Objects of class NWA can be created from new("NWA", pvalues, phenotypes=NULL, interactome=NULL) (see the examples below)

Slots

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.

Methods

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.

Author(s)

Xin Wang [e-mail]

See Also

preprocess analyze summarize interactome viewSubNet plotSubNet report

Examples

## 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)

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.