R Bioconductor找不到ChipDb类的keys（）函数

你好，Bioconductor用户

我正在玩ChipDb类，特别是illuminaHumanv4.db包。我只是尝试使用select方法从该db创建注释表，如帮助部分所述

我相信唯一需要测试的库是

library("illuminaHumanv4.db")

cols函数工作正常

    > cols(illuminaHumanv4.db)
 [1] "PROBEID"      "ENTREZID"     "PFAM"         "IPI"          "PROSITE"      "ACCNUM"       "ALIAS"        "CHR"          "CHRLOC"       "CHRLOCEND"   
[11] "ENZYME"       "MAP"          "PATH"         "PMID"         "REFSEQ"       "SYMBOL"       "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
[21] "GENENAME"     "UNIPROT"      "GO"           "EVIDENCE"     "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL"  "OMIM"         "UCSCKG"

keytypes函数也可以正常工作

    > keytypes(illuminaHumanv4.db)
 [1] "ENTREZID"     "PFAM"         "IPI"          "PROSITE"      "ACCNUM"       "ALIAS"        "CHR"          "CHRLOC"       "CHRLOCEND"    "ENZYME"      
[11] "MAP"          "PATH"         "PMID"         "REFSEQ"       "SYMBOL"       "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "GENENAME"    
[21] "UNIPROT"      "GO"           "EVIDENCE"     "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL"  "PROBEID"      "OMIM"         "UCSCKG"

但是，当我运行keys函数时，我得到以下错误

    > keys(illuminaHumanv4.db)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘keys’ for signature ‘"ChipDb"’

根据文档，ChipDb类应从AnnotationDb类继承此函数。当我尝试运行select函数时，这会导致一个错误，因为要传递的参数之一是由keys函数生成的

我已经更新了我的环境R3.0.1、bioconductor 2.12和我的所有软件包，这是我的会话信息

    R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] grid      splines   parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu95av2.db_2.9.0         BiocInstaller_1.10.2      gplots_2.11.3             KernSmooth_2.23-10        caTools_1.14              gdata_2.13.2             
 [7] gtools_3.0.0              hash_2.2.6                shiny_0.6.0               GO.db_2.9.0               illuminaHumanv4.db_1.18.0 org.Hs.eg.db_2.9.0       
[13] RSQLite_0.11.4            DBI_0.2-7                 annotate_1.38.0           AnnotationDbi_1.22.6      genefilter_1.42.0         WGCNA_1.27-1             
[19] doParallel_1.0.3          iterators_1.0.6           foreach_1.4.1             MASS_7.3-27               reshape_0.8.4             plyr_1.8                 
[25] cluster_1.14.4            Hmisc_3.12-2              survival_2.37-4           flashClust_1.01-2         dynamicTreeCut_1.21       impute_1.34.0            
[31] Biobase_2.20.1            BiocGenerics_0.6.0       

loaded via a namespace (and not attached):
 [1] AnnotationForge_1.2.2 bitops_1.0-5          codetools_0.2-8       compiler_3.0.1        digest_0.6.3          httpuv_1.0.6.3        IRanges_1.18.2       
 [8] lattice_0.20-15       Rcpp_0.10.4           RJSONIO_1.0-3         stats4_3.0.1          tools_3.0.1           XML_3.95-0.2          xtable_1.7-1

如果最近有人遇到同样的问题，请告诉我

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谢谢大家!

这里有一些BioC用户，但是如果您编辑了问题，包括将该问题设置为可复制问题所需的库调用，您可能会获得更广泛的受众。我们大多数人都不知道在哪里可以找到这些函数。谢谢你。我在顶部添加了库调用。嗯，我遇到了错误，需要更新到R版本3.0.1的当前版本。当我这样做的时候，我没有出错。我有48106+1把钥匙。您似乎没有补丁版本。也许重新启动并只加载所需的包是明智的？你现在加载的包比我多11个。实际上，另外我需要的选择方法是在2个包MASS和AnnotationDBi中定义的，所以确保使用AnnotationDBi:：selectI最终解决了问题。它根本不在补丁版本中。原来我有另一个R应用程序——Shining应用程序，它显示了调用libraryhash的另一个应用程序生成的数据，libraryhash也定义了一个keys函数。同样，这是一个函数名冲突。解决此问题的最佳方法是再次在keys函数：AnnotationDBi:：keys上预先添加包。在我看来，面向对象编程的另一个要点。