class "DAVIDTermCluster

Description

This class represents the output of a DAVID Functional Annotation Clustering report.

Type

This class is a "Concrete" one.

Extends

• DAVIDCluster and uses its constructor to parse the report.

Slots

the ones inherited from DAVIDCluster.

Methods

initialize

signature(.Object="DAVIDTermCluster", fileName="character"): basic cluster report file parser.

DAVIDTermCluster

signature(fileName="character"): high level gene cluster report file parser.

ids

signature(object="DAVIDTermCluster"): list with the member ids within each cluster.

plot2D

signature(object="DAVIDTermCluster", number=1, color=c("FALSE"="black","TRUE"="green")): ggplot2 tile plot of genes vs functional annotation category membership of the given cluster number.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175

See Also

Other DAVIDTermCluster: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, ids, ids, ids, ids, ids, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Examples

{
##Load the Gene Functional Classification Tool file report for the
##input demo file 2 to create a DAVIDGeneCluster object.
setwd(tempdir())
fileName<-system.file("files/termClusterReport2.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))
davidTermCluster2

##Now we can invoke DAVIDCluster ancestor functions to inspect the report
##data, of each cluster. For example, we can call summary to get a general
##idea, and the inspect the cluster with higher Enrichment Score, to see
##which members belong to it, etc. Or simply returning the whole cluster as a
##list with EnrichmentScore and Members.
summary(davidTermCluster2)
higherEnrichment<-which.max(enrichment(davidTermCluster2))
clusterGenes<-members(davidTermCluster2)[[higherEnrichment]]
wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]]

##Then, we can obtain the ids of the term members calling clusterGenes object
##which is a DAVIDFunctionalAnnotationChart class or directly using ids on
##davidTermCluster2 for the higherEnrichment cluster.
ids(clusterGenes)
ids(davidTermCluster2)[[higherEnrichment]]

##Finally, we can inspect a 2D tile membership plot, to visual inspect for
##overlapping of genes across the term members of the selected cluster.
plot2D(davidTermCluster2, number=higherEnrichment)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RDAVIDWebService)
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GOstats
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand



Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: ggplot2

Attaching package: 'RDAVIDWebService'

The following object is masked from 'package:AnnotationDbi':

    species

The following object is masked from 'package:IRanges':

    members

The following objects are masked from 'package:BiocGenerics':

    counts, species

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RDAVIDWebService/DAVIDTermCluster-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DAVIDTermCluster-class
> ### Title: class "DAVIDTermCluster
> ### Aliases: DAVIDTermCluster-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> {
+ ##Load the Gene Functional Classification Tool file report for the
+ ##input demo file 2 to create a DAVIDGeneCluster object.
+ setwd(tempdir())
+ fileName<-system.file("files/termClusterReport2.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE))
+ davidTermCluster2
+ 
+ ##Now we can invoke DAVIDCluster ancestor functions to inspect the report
+ ##data, of each cluster. For example, we can call summary to get a general
+ ##idea, and the inspect the cluster with higher Enrichment Score, to see
+ ##which members belong to it, etc. Or simply returning the whole cluster as a
+ ##list with EnrichmentScore and Members.
+ summary(davidTermCluster2)
+ higherEnrichment<-which.max(enrichment(davidTermCluster2))
+ clusterGenes<-members(davidTermCluster2)[[higherEnrichment]]
+ wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]]
+ 
+ ##Then, we can obtain the ids of the term members calling clusterGenes object
+ ##which is a DAVIDFunctionalAnnotationChart class or directly using ids on
+ ##davidTermCluster2 for the higherEnrichment cluster.
+ ids(clusterGenes)
+ ids(davidTermCluster2)[[higherEnrichment]]
+ 
+ ##Finally, we can inspect a 2D tile membership plot, to visual inspect for
+ ##overlapping of genes across the term members of the selected cluster.
+ plot2D(davidTermCluster2, number=higherEnrichment)
+ }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>