{
##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)
}
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-categories.Rd_%03d_medium.png", width=480, height=480)
> ### Name: categories
> ### Title: 'categories' for the different DAVIDWebService package class
> ### objects
> ### Aliases: categories,DAVIDFunctionalAnnotationChart-method
> ### categories,DAVIDFunctionalAnnotationTable-method categories
>
> ### ** 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)
+ }
[1] "GOTERM_BP_ALL" "GOTERM_CC_ALL" "GOTERM_MF_ALL" "KEGG_PATHWAY"
>
>
>
>
>
> dev.off()
null device
1
>