Basic console output

Description

The different implementations of show function for the DAVIDWebService package classes.

Usage

  ## S4 method for signature 'DAVIDResult'
show(object)

  ## S4 method for signature 'DAVIDGenes'
show(object)

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

  ## S4 method for signature 'DAVIDCluster'
show(object)

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

  ## S4 method for signature 'DAVIDWebService'
show(object)

Arguments

Value

Basic console output.

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 only the head of the
##loaded data.frame geneList1 (just to keep it simple).
data(geneList1)
davidGenes1<-DAVIDGenes(head(geneList1))
davidGenes1

##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 head of the loaded data.frame funChart2 (just to keep
##it simple).
data(funChart2)
davidFunChart2<-DAVIDFunctionalAnnotationChart(head(funChart2))
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)
davidFunTable1
}

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-show.Rd_%03d_medium.png", width=480, height=480)
> ### Name: show
> ### Title: Basic console output
> ### Aliases: show,DAVIDCluster-method
> ###   show,DAVIDFunctionalAnnotationChart-method
> ###   show,DAVIDFunctionalAnnotationTable-method show,DAVIDGenes-method
> ###   show,DAVIDResult-method show,DAVIDWebService-method show
> 
> ### ** Examples
> 
> {
+ ##DAVIDGenes example:
+ ##Load Show Gene List file report for the input demo file 1, using data
+ ##function. Then, create a DAVIDGenes object using only the head of the
+ ##loaded data.frame geneList1 (just to keep it simple).
+ data(geneList1)
+ davidGenes1<-DAVIDGenes(head(geneList1))
+ davidGenes1
+ 
+ ##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 head of the loaded data.frame funChart2 (just to keep
+ ##it simple).
+ data(funChart2)
+ davidFunChart2<-DAVIDFunctionalAnnotationChart(head(funChart2))
+ 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)
+ davidFunTable1
+ }
DAVID Result object
Result type:  Functional Annotation Table 
Genes: 149  with (unique: 141 , duplicate: 8 )
Available categories:  GOTERM_BP_ALL, GOTERM_CC_ALL, GOTERM_MF_ALL, KEGG_PATHWAY 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>