Mercurial > repos > kpbioteam > clusterprofiler_go
view clusterProfiler_go.R @ 4:3d18046320ce draft
planemo upload for repository https://github.com/kpbioteam/clusterProfiler_go commit 19aa66aed9f704dc98680d2573ff7b13c81c0ca2-dirty
author | kpbioteam |
---|---|
date | Sun, 15 Jul 2018 10:47:56 -0400 |
parents | 7a6ba13c9381 |
children | a12bbeb898a4 |
line wrap: on
line source
require("clusterProfiler", quietly = TRUE) require("DO.db", quietly = TRUE) require("org.Hs.eg.db", quietly = TRUE) require("ggplot2", quietly = TRUE) args <- commandArgs(trailingOnly = TRUE) input1 = args[1] output1 = args[2] output2 = args[3] gene <- read.table(input1) ego <- enrichGO(gene = c(gene$V1), keyType = "ENTREZID", OrgDb = org.Hs.eg.db, ont = "BP", pAdjustMethod = "BH", pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = TRUE) write.table(ego, output1) dotplot(ego) ggsave(file = output2, device = "pdf", width = 21, height = 29, units = "cm")