KEGG pathway analysis with ReportingTools
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@mayte-suarez-farinas-2068
Last seen 6.4 years ago
United States
Dear All, I am successfully using the ReportingTools package to detect over- expressed categories using hypergeometric Test for Gene Ontologies and PFAM follwoing the package vignette. When I tried to do the same using KEGG pathways, the function publish does not work. I am surprise because class PFAMHyperGResult and KEGGHyperGResult have the same structure. Can anyone shed light onto this? Mayte ### CODE > keggParams<-new("KEGGHyperGParams", geneIds = DEGi_entrez, universeGeneIds=UnivEntrez, + annotation='hgu133plus2.db', pvalueCutoff = 0.1, testDirection = "over") Warning in makeValidParams(.Object) : removing duplicate IDs in universeGeneIds > keggResults<-hyperGTest(keggParams) > keggtab <-HTMLReport(shortName = paste("KEGG Analysis",cni_original,sep=''), + title='KEGG Analysis', reportDirectory="./reports") > publish(keggResults, keggtab, selectedIDs=DEGi_entrez, annotation.db="org.Hs.eg",categorySize=10, makePlot=FALSE) Error in as.data.frame.default(object, "data.frame") : cannot coerce class "structure("KEGGHyperGResult", package = "Category")" to a data.frame > sessionInfo() 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] splines grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] EMA_1.4.4 PFAM.db_2.9.0 proto_0.3-10 Category_2.26.0 hwriter_1.3 [6] lattice_0.20-24 affycoretools_1.32.1 KEGG.db_2.9.1 GO.db_2.9.0 ReportingTools_2.0.1 [11] statmod_1.4.18 MASS_7.3-29 hgu133plus2.db_2.9.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.4 [16] DBI_0.2-7 genefilter_1.42.0 car_2.0-19 Rcmdr_2.0-4 RcmdrPlugin.KMggplot2_0.2-0 [21] ggplot2_0.9.3.1 mgcv_1.7-28 nlme_3.1-113 rgl_0.93.996 hgu133plus2probe_2.12.0 [26] hgu133plus2cdf_2.12.0 AnnotationDbi_1.22.6 plyr_1.8 gcrma_2.32.0 gdata_2.13.2 [31] limma_3.16.8 affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affyio_1.28.0 annaffy_1.32.0 annotate_1.38.0 AnnotationForge_1.2.2 BiocInstaller_1.10.4 biomaRt_2.16.0 [7] Biostrings_2.28.0 biovizBase_1.8.1 bit_1.1-11 bitops_1.0-6 BSgenome_1.28.0 caTools_1.16 [13] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 edgeR_3.2.4 [19] FactoMineR_1.25 ff_2.2-12 foreach_1.4.1 Formula_1.1-1 GenomicFeatures_1.12.4 GenomicRanges_1.12.5 [25] ggbio_1.8.8 ggthemes_1.6.0 GOstats_2.26.0 gplots_2.12.1 graph_1.38.3 gridExtra_0.9.1 [31] GSA_1.03 GSEABase_1.22.0 gtable_0.1.2 gtools_3.3.0 heatmap.plus_1.3 Hmisc_3.14-0 [37] IRanges_1.18.4 iterators_1.0.6 KernSmooth_2.23-10 labeling_0.2 latticeExtra_0.6-26 Matrix_1.1-2 [43] multtest_2.16.0 munsell_0.4.2 nnet_7.3-7 oligoClasses_1.22.0 preprocessCore_1.22.0 R.methodsS3_1.6.1 [49] R.oo_1.17.0 R.utils_1.29.8 R2HTML_2.2.1 RBGL_1.36.2 RColorBrewer_1.0-5 RCurl_1.95-4.1 [55] reshape2_1.2.2 Rsamtools_1.12.4 rtracklayer_1.20.4 scales_0.2.3 siggenes_1.34.0 stats4_3.0.1 [61] stringr_0.6.2 survival_2.37-7 tcltk_3.0.1 tcltk2_1.2-10 tools_3.0.1 VariantAnnotation_1.6.8 [67] XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 Mayte Suarez-Farinas, PhD Research Assistant Professor Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178 New York, NY 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232
Pathways GO ReportingTools Pathways GO ReportingTools • 832 views
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