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Question: Using Pathview with gene.idtype = "SYMBOL"
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gravatar for sofia.figueiredo
13 months ago by
sofia.figueiredo10 wrote:

Dear Bioconductor community,

I want to map my FC data to a Pathway using pathview like this:

> pv.out <- pathview(gene.data = Nn.matrix[, 1], gene.idtype = "SYMBOL", pathway.id = "04110", species = "hsa", out.suffix = "Nn", kegg.native = TRUE)

However, I get the following error:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.
Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.

My gene.data is a matrix, where the rownames are the gene symbol:

> head(Nn.matrix[, 1])
  "CISH"   "PIM1"  "SOCS1" "MTHFD2"  "DUSP6" "SLC7A5" 
  4.4023   2.0829   3.7926   2.1230   3.4521   3.1203 

Does anyone know why Pathview is not working in this case? I appreciate your attention.

Thanks in advance,

Sofia

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] KEGGREST_1.12.2                      maanova_1.42.0                       multtest_2.28.0                     
 [4] factDesign_1.48.0                    statmod_1.4.25                       mdgsa_1.4.2                         
 [7] plyr_1.8.4                           data.table_1.9.6                     ComplexHeatmap_1.10.2               
[10] vegan_2.4-0                          lattice_0.20-33                      permute_0.9-0                       
[13] Heatplus_2.18.0                      RColorBrewer_1.1-2                   gplots_3.0.1                        
[16] GO.db_3.3.0                          annotate_1.50.0                      XML_3.98-1.4                        
[19] reactome.db_1.55.0                   KEGG.db_3.2.3                        limma_3.28.19                       
[22] SCAN.UPC_2.14.0                      sva_3.20.0                           genefilter_1.54.2                   
[25] mgcv_1.8-14                          nlme_3.1-128                         foreach_1.4.3                       
[28] affyio_1.42.0                        affy_1.50.0                          GEOquery_2.38.4                     
[31] hugene20sttranscriptcluster.db_8.4.0 hugene20stprobeset.db_8.4.0          arrayQualityMetrics_3.28.2          
[34] pathview_1.12.0                      org.Hs.eg.db_3.3.0                   AnnotationDbi_1.34.4                
[37] GenomicRanges_1.24.2                 GenomeInfoDb_1.8.3                   pd.hugene.2.0.st_3.14.1             
[40] oligo_1.36.1                         Biobase_2.32.0                       oligoClasses_1.34.0                 
[43] RSQLite_1.0.0                        DBI_0.5                              Biostrings_2.40.2                   
[46] XVector_0.12.1                       IRanges_2.6.1                        S4Vectors_0.10.3                    
[49] BiocGenerics_0.18.0                  BiocInstaller_1.22.3                

loaded via a namespace (and not attached):
 [1] colorspace_1.2-6           rjson_0.2.15               hwriter_1.3.2              class_7.3-14               modeltools_0.2-21         
 [6] mclust_5.2                 circlize_0.3.8             GlobalOptions_0.0.10       base64_2.0                 flexmix_2.3-13            
[11] mvtnorm_1.0-5              codetools_0.2-14           splines_3.3.1              robustbase_0.92-6          Formula_1.2-1             
[16] Cairo_1.5-9                kernlab_0.9-24             cluster_2.0.4              vsn_3.40.0                 png_0.1-7                 
[21] graph_1.50.0               httr_1.2.1                 Matrix_1.2-6               SVGAnnotation_0.93-1       BeadDataPackR_1.24.2      
[26] acepack_1.3-3.3            tools_3.3.1                gtable_0.2.0               reshape2_1.4.1             affxparser_1.44.0         
[31] Rcpp_0.12.6                trimcluster_0.1-2          RJSONIO_1.3-0              gdata_2.17.0               preprocessCore_1.34.0     
[36] setRNG_2013.9-1            iterators_1.0.8            fpc_2.1-10                 stringr_1.1.0              affyPLM_1.48.0            
[41] gtools_3.5.0               dendextend_1.2.0           DEoptimR_1.0-6             zlibbioc_1.18.0            MASS_7.3-45               
[46] scales_0.4.0               SummarizedExperiment_1.2.3 KEGGgraph_1.30.0           beadarray_2.22.2           curl_1.2                  
[51] gridExtra_2.2.1            ggplot2_2.1.0              rpart_4.1-10               latticeExtra_0.6-28        stringi_1.1.1             
[56] gcrma_2.44.0               gridSVG_1.5-0              caTools_1.17.1             shape_1.4.2                chron_2.3-47              
[61] prabclus_2.2-6             bitops_1.0-6               bit_1.1-12                 magrittr_1.5               R6_2.1.3                  
[66] Hmisc_3.17-4               whisker_0.3-2              foreign_0.8-66             survival_2.39-5            RCurl_1.95-4.8            
[71] nnet_7.3-12                KernSmooth_2.23-15         GetoptLong_0.1.4           Rgraphviz_2.16.0           diptest_0.75-7            
[76] xtable_1.8-2               ff_2.2-13                  illuminaio_0.14.0          openssl_0.9.4              munsell_0.4.3    

 

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