NWA-class {HTSanalyzeR} | R Documentation

## An S4 class for NetWork Analysis on 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 xw264@cam.ac.uk

### 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)

[Package HTSanalyzeR version 2.38.0 Index]