DAVIDClasses-categories: 'categories' for the different DAVIDWebService package class...

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description

Obtain ids related information, according to the given function call (see Values).

Usage

  categories(object)

  ## S4 method for signature 'DAVIDFunctionalAnnotationChart'
categories(object)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
categories(object)

Arguments

object

DAVIDWebService class object. Possible values are: DAVIDFunctionalAnnotationChart or DAVIDFunctionalAnnotationTable.

Value

according to the call, one of the following objects can be returned:

DAVIDFunctionalAnnotationChart	factor vector of the "Category" column.
DAVIDFunctionalAnnotationTable	character vector with the name of available main categories in the dictionary/membership.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

Other DAVIDFunctionalAnnotationChart: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart-class, 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

Other DAVIDFunctionalAnnotationTable: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable-class, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, dictionary, dictionary, genes, genes, genes, genes, initialize, initialize, initialize, initialize, initialize, initialize, initialize, membership, membership, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D, subset, subset

Examples

{
##DAVIDFunctionalAnnotationChart example
##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.
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)

##DAVIDFunctionalAnnotationTable example
##Load the Functional Annotation Table file report for the input demo
##file 1, using data function. Then, create a DAVIDFunctionalAnnotationTable
##object using the loaded data.frame annotationTable1.
data(annotationTable1)
davidFunTable1<-DAVIDFunctionalAnnotationTable(annotationTable1)

##Now, the user can inspect the main categories used in the analysis.
categories(davidFunTable1)
}

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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 object is masked from 'package:base':

    expand.grid

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

[1] "GOTERM_BP_ALL" "GOTERM_CC_ALL" "GOTERM_MF_ALL" "KEGG_PATHWAY" 

RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.