require(ReactomePA)
load("cache/gene.rda")
eg=bitr(gene, "ENSEMBL", "ENTREZID", "org.Hs.eg.db")[, "ENTREZID"]
## Warning in bitr(gene, "ENSEMBL", "ENTREZID", "org.Hs.eg.db"): 2.83% of
## input gene IDs are fail to map...
rr <- enrichPathway(eg, readable=TRUE)
dim(summary(rr))
## [1] 56 9
head(summary(rr)[,-8])
## ID
## 192823 192823
## 72689 72689
## 156902 156902
## 72764 72764
## 156842 156842
## 975956 975956
## Description
## 192823 Viral mRNA Translation
## 72689 Formation of a pool of free 40S subunits
## 156902 Peptide chain elongation
## 72764 Eukaryotic Translation Termination
## 156842 Eukaryotic Translation Elongation
## 975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
## GeneRatio BgRatio pvalue p.adjust qvalue Count
## 192823 25/107 86/6750 7.462910e-26 2.253324e-23 1.627641e-23 25
## 72689 26/107 98/6750 9.994051e-26 2.253324e-23 1.627641e-23 26
## 156902 25/107 88/6750 1.428415e-25 2.253324e-23 1.627641e-23 25
## 72764 25/107 88/6750 1.428415e-25 2.253324e-23 1.627641e-23 25
## 156842 25/107 91/6750 3.659323e-25 4.618065e-23 3.335761e-23 25
## 975956 25/107 93/6750 6.710543e-25 7.057254e-23 5.097658e-23 25
dotplot(rr)
date()
## [1] "Fri Jul 17 15:12:02 2015"
sessionInfo()
## R version 3.2.1 (2015-06-18)
## Platform: x86_64-apple-darwin14.3.0 (64-bit)
## Running under: OS X 10.10.4 (Yosemite)
##
## 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] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] ReactomePA_1.13.2 org.Hs.eg.db_3.1.2 DO.db_2.9
## [4] RDAVIDWebService_1.6.0 ggplot2_1.0.1 GOstats_2.34.0
## [7] Category_2.34.2 GO.db_3.1.2 AnnotationDbi_1.30.1
## [10] GenomeInfoDb_1.4.1 IRanges_2.2.5 S4Vectors_0.6.1
## [13] Matrix_1.2-2 Biobase_2.28.0 BiocGenerics_0.14.0
## [16] graph_1.46.0 clusterProfiler_2.3.6 DOSE_2.7.9
## [19] RSQLite_1.0.0 DBI_0.3.1 rmarkdown_0.7
## [22] roxygen2_4.1.1 magrittr_1.5 BiocInstaller_1.18.3
##
## loaded via a namespace (and not attached):
## [1] KEGGREST_1.8.0 qvalue_2.0.0 genefilter_1.50.0
## [4] reshape2_1.4.1 rJava_0.9-6 splines_3.2.1
## [7] lattice_0.20-31 tcltk_3.2.1 graphite_1.15.0
## [10] colorspace_1.2-6 htmltools_0.2.6 XML_3.98-1.3
## [13] RBGL_1.44.0 survival_2.38-3 topGO_2.20.0
## [16] plyr_1.8.3 stringr_1.0.0 zlibbioc_1.14.0
## [19] Biostrings_2.36.1 munsell_0.4.2 GOSemSim_1.27.4
## [22] gtable_0.1.2 evaluate_0.7 labeling_0.3
## [25] knitr_1.10.5 SparseM_1.6 GSEABase_1.30.2
## [28] proto_0.3-10 Rcpp_0.11.6 reactome.db_1.52.1
## [31] xtable_1.7-4 scales_0.2.5 formatR_1.2
## [34] annotate_1.46.1 XVector_0.8.0 png_0.1-7
## [37] digest_0.6.8 stringi_0.4-1 grid_3.2.1
## [40] tools_3.2.1 MASS_7.3-42 httr_1.0.0
## [43] AnnotationForge_1.10.1 R6_2.1.0 igraph_1.0.1
