[BioC] KEGG pathway analysis with ReportingTools

Tue Apr 8 21:35:18 CEST 2014

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