getURL.RdThis function highlights the genes involved in the present GPS for a pathway of interest in its diagram. Please note that this functionality is only implemented for results of Reactome or KEGG based analyses.
getURL(yy, i)
| yy | A sigora analysis result object (created by |
|---|---|
| i | The rank position of the pathway of interest in summary_results. |
The URL of the pathway diagram, where the relevant genes from your original query list are highlighted.
data('kegH') set.seed(seed=12345) a1<-genesFromRandomPathways(kegH,3,50) #> ### randomly selected pathways are: #> hsa04218 #> hsa00590 #> hsa04917 ## originally selected pathways:\cr a1[["selectedPathways"]] #> [1] "hsa04218" "hsa00590" "hsa04917" ## what are the genes a1[["genes"]] #> [1] "9134" "91860" "5499" "22800" "1111" "90550" #> [7] "6776" "1874" "8792" "4051" "28996" "22808" #> [13] "1557" "890" "5594" "493869" "5606" "8600" #> [19] "2876" "100137049" "83447" "894" "1030" "1559" #> [25] "11145" "4773" "1573" "4893" "7248" "5296" #> [31] "293" "3708" "2053" "147746" "874" "1081" #> [37] "23291" "3803" "8681" "292" "2878" "2678" #> [43] "391013" "824" "5605" "3972" "4616" "85417" #> [49] "891" "5291" ## sigora's results with this input:\cr sigoraRes <- sigora(GPSrepo =kegH, queryList = a1[["genes"]],level = 2) #> pathwy.id description pvalues Bonferroni successes #> 1 hsa04218 Cellular senescence 1.669e-108 5.090e-106 56.68 #> 2 hsa00590 Arachidonic acid metabolism 3.125e-41 9.531e-39 21.83 #> PathwaySize N sample.size #> 1 2037.98 452219.2 87.58 #> 2 606.97 452219.2 87.58 ## Diagram for the most significant result, where the genes from our list are highlighted in red: getURL(sigoraRes,1) #> assuming this is a result from KEGG ... #> [1] "https://www.genome.jp/kegg-bin/show_pathway?hsa04218+HIPK2+HIPK4+MCU+KIR2DL2+E2F4+CCNB3+FBXW11+CAPN2+RRAS2+MRAS+TSC1+CHEK1+CCNB1+MAP2K3+CDKN2B+SLC25A5+SLC25A6+SLC25A31+CCNA2+NFATC2+PPP1CA+GADD45B+ITPR1+CALML4+CCNE2+CCND2+MAP2K2+NRAS+PIK3CB+PIK3R2+MAPK1"