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Valueaccording to the call, one of the following objects can be returned:
Author(s)Cristobal Fresno and Elmer A Fernandez See AlsoOther DAVIDCluster: Other DAVIDCluster: Other DAVIDCluster: Examples{ ##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)) davidGeneCluster1 ##Now we can invoke DAVIDCluster ancestor functions to inspect the report ##data of each cluster. For example, we can call summary to get a general ##idea, and then inspect the cluster with the higher Enrichment Score, to see ##which members belong to it, etc. or simply, returning the whole cluster as ##a list with EnrichmentScore and Members. summary(davidGeneCluster1) higherEnrichment<-which.max(enrichment(davidGeneCluster1)) clusterGenes<-members(davidGeneCluster1)[[higherEnrichment]] wholeCluster<-cluster(davidGeneCluster1)[[higherEnrichment]] ##DAVIDTermCluster example: ##Load the Gene Functional Classification Tool file report for the ##input demo file 2 to create a DAVIDGeneCluster object. setwd(tempdir()) fileName<-system.file("files/termClusterReport2.tab.tar.gz", package="RDAVIDWebService") untar(fileName) davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE)) davidTermCluster2 ##Now we can invoke DAVIDCluster ancestor functions to inspect the report ##data of each cluster. For example, we can call summary to get a general ##idea, and then inspect the cluster with the higher Enrichment Score, to see ##which members belong to it, etc. Or simply returning the whole cluster as a ##list with EnrichmentScore and Members. summary(davidTermCluster2) higherEnrichment<-which.max(enrichment(davidTermCluster2)) clusterGenes<-members(davidTermCluster2)[[higherEnrichment]] wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]] } ResultsR 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/DAVIDCluster-methods.Rd_%03d_medium.png", width=480, height=480) > ### Name: cluster > ### Title: Methods for 'DAVIDCluster' class object > ### Aliases: cluster,DAVIDCluster-method cluster-methods > ### enrichment,DAVIDCluster-method members,DAVIDCluster-method cluster > ### enrichment members > > ### ** Examples > > { + ##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)) + davidGeneCluster1 + + ##Now we can invoke DAVIDCluster ancestor functions to inspect the report + ##data of each cluster. For example, we can call summary to get a general + ##idea, and then inspect the cluster with the higher Enrichment Score, to see + ##which members belong to it, etc. or simply, returning the whole cluster as + ##a list with EnrichmentScore and Members. + summary(davidGeneCluster1) + higherEnrichment<-which.max(enrichment(davidGeneCluster1)) + clusterGenes<-members(davidGeneCluster1)[[higherEnrichment]] + wholeCluster<-cluster(davidGeneCluster1)[[higherEnrichment]] + + + ##DAVIDTermCluster example: + ##Load the Gene Functional Classification Tool file report for the + ##input demo file 2 to create a DAVIDGeneCluster object. + setwd(tempdir()) + fileName<-system.file("files/termClusterReport2.tab.tar.gz", + package="RDAVIDWebService") + untar(fileName) + davidTermCluster2<-DAVIDTermCluster(untar(fileName, list=TRUE)) + davidTermCluster2 + + ##Now we can invoke DAVIDCluster ancestor functions to inspect the report + ##data of each cluster. For example, we can call summary to get a general + ##idea, and then inspect the cluster with the higher Enrichment Score, to see + ##which members belong to it, etc. Or simply returning the whole cluster as a + ##list with EnrichmentScore and Members. + summary(davidTermCluster2) + higherEnrichment<-which.max(enrichment(davidTermCluster2)) + clusterGenes<-members(davidTermCluster2)[[higherEnrichment]] + wholeCluster<-cluster(davidTermCluster2)[[higherEnrichment]] + } > > > > > > dev.off() null device 1 > |
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