class "DAVIDFunctionalAnnotationChart

Description

This class represents the output of "Functional Annotation Chart" of DAVID. It is an heir of DAVIDResult in the conceptual way, and also a data.frame with additional features, such as identifying the unique and duplicate ids, searching for genes with a given id, etc.

Type

This class is a "Concrete" one.

Extends

• DAVIDResult in the conceptual way.

• data.frame in order to extend the basic features.

Slots

no additional to the ones inherited from DAVIDResult and data.frame classes.

Methods

show

signature(object="DAVIDFunctionalAnnotationChart"): returns a basic console output.

valid

signature(object="DAVIDFunctionalAnnotationChart") : logical which checks DAVID's file output name ("Category", "Term", "Count", etc.) presence.

DAVIDFunctionalAnnotationChart

signature( object="character"): constructor with the name of the .tab file report to load.

DAVIDFunctionalAnnotationChart

signature( object="data.frame"): data.frame already loaded to use when constructing the object.

as

signature(object="DAVIDFunctionalAnnotationChart"): coerce a data.frame into a DAVIDFunctionalAnnotationChart object.

categories

signature( object="DAVIDFunctionalAnnotationChart"): obtain the factor vector of the "Category" column.

ids

signature(object="DAVIDFunctionalAnnotationChart"): obtain a list with character/integer vector with the ids of the corresponding term.

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

Examples

{
##Load the Functional Annotation Chart file report for the input demo
##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
## object using the loaded data.frame funChart2. In addition, the user can
##use the file name of the downloaded file report.
data(funChart2)
davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)

##In Addition to the usual data.frame accessors, the user can inspect the
##main categories used in the analysis.
categories(davidFunChart2)

##Obtain the ids of the genes present in each Term, as a list of character
##vector
ids(davidFunChart2)

##Or plot a 2D tile matrix with the reported evidence (green) or not (black).
##Just to keep it simple, for the first five terms present in funChart2
##object.
plot2D(DAVIDFunctionalAnnotationChart(funChart2[1:5, ]),
color=c("FALSE"="black", "TRUE"="green"))
}

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/DAVIDFunctionalAnnotationChart-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DAVIDFunctionalAnnotationChart-class
> ### Title: class "DAVIDFunctionalAnnotationChart
> ### Aliases: DAVIDFunctionalAnnotationChart-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> {
+ ##Load the Functional Annotation Chart file report for the input demo
+ ##file 2, using data function. Then, create a DAVIDFunctionalAnnotationChart
+ ## object using the loaded data.frame funChart2. In addition, the user can
+ ##use the file name of the downloaded file report.
+ data(funChart2)
+ davidFunChart2<-DAVIDFunctionalAnnotationChart(funChart2)
+ 
+ ##In Addition to the usual data.frame accessors, the user can inspect the
+ ##main categories used in the analysis.
+ categories(davidFunChart2)
+ 
+ ##Obtain the ids of the genes present in each Term, as a list of character
+ ##vector
+ ids(davidFunChart2)
+ 
+ ##Or plot a 2D tile matrix with the reported evidence (green) or not (black).
+ ##Just to keep it simple, for the first five terms present in funChart2
+ ##object.
+ plot2D(DAVIDFunctionalAnnotationChart(funChart2[1:5, ]),
+ color=c("FALSE"="black", "TRUE"="green"))
+ }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>