DAVIDFunctionalAnnotationTable-methods: Methods for 'DAVIDFunctionalAnnotationTable' class object

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

Description

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

Usage

  subset(x, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
subset(x,selection=c("Membership",
  "Dictionary"), category, drop=TRUE)

  dictionary(object, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
dictionary(object,
  ...)

  membership(object, ...)

  ## S4 method for signature 'DAVIDFunctionalAnnotationTable'
membership(object,
  ...)

Arguments

object,x	DAVIDFunctionalAnnotationTable class object.
selection	which slot to use to obtain the subset. Possible values are "Membership" or "Dictionary".
category	named list with main annotation category, which contains a character vector with the ids to use. Default value is missing in order to use all available categories of the report.
drop	Should list structure be drop if length==1? Default value TRUE.
...	Additional parameters for subset function call.

Value

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

subset	list with filtered categories/ids according to function call.
enrichment	numeric vector with DAVID cluster's enrichment score.
members	list with DAVID Cluster's members.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

Other DAVIDCluster: DAVIDCluster-class, cluster, cluster, enrichment, enrichment, members, members, summary, summary, summary, summary

Other DAVIDFunctionalAnnotationTable: DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationChart, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable, DAVIDFunctionalAnnotationTable-class, DAVIDGODag, DAVIDGODag, DAVIDGeneCluster, DAVIDGeneCluster, DAVIDGenes, DAVIDGenes, DAVIDGenes, DAVIDTermCluster, DAVIDTermCluster, as, as, as, categories, categories, categories, genes, genes, genes, genes, 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, categories, categories, categories, genes, genes, genes, genes, initialize, initialize, initialize, initialize, initialize, initialize, initialize, plot2D, plot2D, plot2D, plot2D, plot2D, plot2D

Examples

{
##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)

##Obtain the head of the dictionary and the membership matrix for the first
##annotated genes used in davidFunTable1 object.
head(membership(davidFunTable1, categories(davidFunTable1)[1]))
head(dictionary(davidFunTable1, categories(davidFunTable1)[1]))
head(genes(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, cbind, colMeans, colSums, 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, 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

          ID                                                   Name
1   37166_at                  3-hydroxyanthranilate 3,4-dioxygenase
2 34467_g_at             5-hydroxytryptamine (serotonin) receptor 4
3 41703_r_at                       A kinase (PRKA) anchor protein 7
4   40350_at                        ADAM metallopeptidase domain 23
5    1575_at ATP-binding cassette, sub-family B (MDR/TAP), member 1
6   40294_at ATP-binding cassette, sub-family B (MDR/TAP), member 9
       Species
1 Homo sapiens
2 Homo sapiens
3 Homo sapiens
4 Homo sapiens
5 Homo sapiens
6 Homo sapiens

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