R Graphical Manual

Browse All

Last data update: 2014.03.03

R: 'genes' for the different DAVIDWebService package class...

genes

R Documentation

`genes` for the different DAVIDWebService package class objects.

Description

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

Usage

  genes(object, ...)

  ## S4 method for signature 'DAVIDGenes'
genes(object,ids)

  ## S4 method for signature 'DAVIDGeneCluster'
genes(object)

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

Arguments

`object`	DAVIDGenes or DAVIDGeneCluster class object.
`ids`	character vector with the ids to fetch.
`...`	Additional parameters for internal functions (if applicable).

Value

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

`DAVIDGenes`	a DAVIDGenes object with the matched genes of ids parameter. If missing, returns all the genes.
`DAVIDGeneCluster`	list with DAVIDGenes objects for each cluster.
`DAVIDFunctionalAnnotationTable`	a DAVIDGenes objects, according to ... parameter used internally on genes(DAVIDGenes, ...).

Author(s)

Cristobal Fresno and Elmer A Fernandez

Examples

{
##DAVIDGenes example:
##Load Show Gene List file report for the input demo file 1, using data
##function. Then, create a DAVIDGenes object using the loaded data.frame
##geneList1.
data(geneList1)
davidGenes1<-DAVIDGenes(geneList1)

##Now, get the genes using the ids look up parameter with the first
##six ids. If ids omitted, all the available are returned.
genes(davidGenes1, ids=head(ids(davidGenes1)))

##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 we can obtain the genes for the given ids, or the complete list if the
##parameter is omitted.
genes(davidFunTable1, id=c("37166_at","41703_r_at"))


##DAVIDGeneCluster example:
##Load the Gene Functional Classification Tool file report for the
##input demo list 1 file to create a DAVIDGeneCluster object.
setwd(tempdir())
fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
package="RDAVIDWebService")
untar(fileName)
davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))

##Then, we can obtain the genes of the first cluster using davidGeneCluster1
##object. Or, using genes on DAVIDGenes class once we get the members of the
##cluster
genes(davidGeneCluster1)[[1]]
genes(members(davidGeneCluster1)[[1]])
}

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/DAVIDClasses-genes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genes
> ### Title: 'genes' for the different DAVIDWebService package class objects.
> ### Aliases: genes,DAVIDFunctionalAnnotationTable-method
> ###   genes,DAVIDGeneCluster-method genes,DAVIDGenes-method genes-methods
> ###   genes
> 
> ### ** Examples
> 
> {
+ ##DAVIDGenes example:
+ ##Load Show Gene List file report for the input demo file 1, using data
+ ##function. Then, create a DAVIDGenes object using the loaded data.frame
+ ##geneList1.
+ data(geneList1)
+ davidGenes1<-DAVIDGenes(geneList1)
+ 
+ ##Now, get the genes using the ids look up parameter with the first
+ ##six ids. If ids omitted, all the available are returned.
+ genes(davidGenes1, ids=head(ids(davidGenes1)))
+ 
+ ##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 we can obtain the genes for the given ids, or the complete list if the
+ ##parameter is omitted.
+ genes(davidFunTable1, id=c("37166_at","41703_r_at"))
+ 
+ 
+ ##DAVIDGeneCluster example:
+ ##Load the Gene Functional Classification Tool file report for the
+ ##input demo list 1 file to create a DAVIDGeneCluster object.
+ setwd(tempdir())
+ fileName<-system.file("files/geneClusterReport1.tab.tar.gz",
+ package="RDAVIDWebService")
+ untar(fileName)
+ davidGeneCluster1<-DAVIDGeneCluster(untar(fileName, list=TRUE))
+ 
+ ##Then, we can obtain the genes of the first cluster using davidGeneCluster1
+ ##object. Or, using genes on DAVIDGenes class once we get the members of the
+ ##cluster
+ genes(davidGeneCluster1)[[1]]
+ genes(members(davidGeneCluster1)[[1]])
+ }
DAVID Result object
Result type:  Gene List Report 
          ID
1 37953_s_at
2   32084_at
3   34436_at
4   40317_at
5   37097_at
                                                                       Name
1                            amiloride-sensitive cation channel 2, neuronal
2 solute carrier family 22 (organic cation/carnitine transporter), member 5
3                     solute carrier family 17 (sodium phosphate), member 3
4                            amiloride-sensitive cation channel 1, neuronal
5                     solute carrier family 17 (sodium phosphate), member 1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

genes for the different DAVIDWebService package class objects.