clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Yu, Guangchuang, Li-Gen Wang, Yanyan Han, and Qing-Yu He. clusterProfiler: An R Package for Comparing Biological Themes Among Gene Clusters. OMICS: A Journal of Integrative Biology 16, no. 5 (May 2012): 284–287.

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  1. 您好!我在安装Reactome时显示:
    错误于read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
    无法打开链结
    此外: 警告信息:
    1: In download.file(url, destfile, method, mode = "wb", ...) :
    下载的长度70724不等于报告的长度265171851
    2: In download.file(url, destfile, method, mode = "wb", ...) :
    下载的长度121849不等于报告的长度124549
    3: In unzip(zipname, exdir = dest) : 从zip文件中抽取1时出了错
    4: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
    无法打开压缩文件'reactome.db/DESCRIPTION',可能是因为'No such file or directory'

    请问如何解决?谢谢!

    Reply

    ygc China Unknow Browser Unknow Os Reply:

    这是reactome.db的问题,你是否通过biocLite安装?

    Reply

  2. Hello, I'm trying to use clusterProfiler to analyze a dataset but it is returning an error I don't understand:

    GOtest <- groupGO(gene = test[[1]], organism = "yeast", ont = "CC", level = 2, readable = TRUE)
    Error in .testIfKeysAreOfProposedKeytype(x, keys, keytype) :
    None of the keys entered are valid keys for the keytype specified.

    Any help with how to address this error would be greatly appreciated.

    Reply

    ygc China Unknow Browser Unknow Os Reply:

    yeast was supported only in the current devel version (bioc 2.13) and the gene ID should be ORF ID.

    Reply

  3. Hi, thank you for getting back to me. I am using the current devel version of bioc. Could you be more specific about what ORF ID I should use?

    When I use the entrez gene id I get the same error:
    test12 <- groupGO(gene=test12entrez[[1]], organism = "yeast", ont="CC", level = 2, readable = TRUE)
    Error in .testIfKeysAreOfProposedKeytype(x, keys, keytype) :
    None of the keys entered are valid keys for the keytype specified.

    When I use either the SGD id or the systematic ORF id I get this error:
    Warning message:
    In EXTID2NAME(genes, organism = organism) :
    the input geneID is not entrezgeneID, and cannot be mapped

    Thank you again for your help

    Reply

    ygc China Unknow Browser Unknow Os Reply:

    please give me some of your sample ID.

    Reply

    Rachel United States Unknow Browser Unknow Os Reply:

    ORF ID: "YAL015C" "YAL018C" "YAL037W" "YAL047C" "YAL059W" "YAL067C"

    SGD ID: "S000003725" "S000006064" "S000006435" "S000004592" "S000000067" "S000007362"

    entrez gene ID: "13393612" "854834" "853357" "853479" "1466473" "854944"

    Thank you!!

    Reply

    ygc China Unknow Browser Unknow Os Reply:

    set readable=FALSE, the mapping from yeast ORF to SYMBOL is not supported yet and will support soon.

    Reply

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