## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, eval = TRUE) ## ----A, echo=TRUE, eval=TRUE, message=FALSE----------------------------------- library(org.Mxanthus.db) ## ----1, echo=TRUE------------------------------------------------------------- keytypes(org.Mxanthus.db) ## ----2, echo=TRUE------------------------------------------------------------- columns(org.Mxanthus.db) ## ----3, echo=TRUE------------------------------------------------------------- select(org.Mxanthus.db, keys="7179", columns=c("SYMBOL","UNIPROT","NAME")) ## ----4------------------------------------------------------------------------ select(org.Mxanthus.db, keys="2000", columns=c("SYMBOL","GO")) ## ----5------------------------------------------------------------------------ select(org.Mxanthus.db, keys="2000", columns=c("SYMBOL","OLD_MXAN")) ## ----6, echo=TRUE, message=FALSE---------------------------------------------- library(DBI) connection <- dbconn(org.Mxanthus.db) ## ----7, echo=TRUE, message=FALSE---------------------------------------------- gene_info <- dbGetQuery(connection, "SELECT * FROM gene_info") go <- dbGetQuery(connection, "SELECT * FROM go") chromosome <- dbGetQuery(connection, "SELECT * FROM chromosome") ## ----8, echo=TRUE, message=FALSE---------------------------------------------- query <- dbGetQuery(connection, "SELECT SYMBOL,NAME FROM gene_info") ## ----9, echo=TRUE, message=FALSE---------------------------------------------- query_2 <- dbGetQuery(connection, "SELECT COUNT(*) FROM gene_info") ## ----10, echo=TRUE, message=FALSE--------------------------------------------- query_3 <- dbGetQuery(connection, "SELECT GO,EVIDENCE,ONTOLOGY FROM go WHERE ONTOLOGY = 'BP'") ## ----11, echo=TRUE, message=FALSE--------------------------------------------- library(clusterProfiler) genes <- exampleGene head(bitr(genes, fromType="SYMBOL", toType="OLD_MXAN", OrgDb=org.Mxanthus.db)) ## ----12, echo=TRUE, eval = TRUE----------------------------------------------- ggo <- groupGO(gene = genes, OrgDb = org.Mxanthus.db, keyType = "SYMBOL", ont = "MF", level = 3) barplot(ggo, drop=TRUE, showCategory=25) ## ----13 , echo=TRUE, eval = TRUE---------------------------------------------- universe <- (dbGetQuery(connection, "SELECT SYMBOL FROM gene_info"))$SYMBOL ego <- enrichGO(gene = genes, universe = universe, keyType = "SYMBOL", OrgDb = org.Mxanthus.db, ont = "BP", pAdjustMethod = "BH", pvalueCutoff = 0.01, qvalueCutoff = 0.05) dotplot(ego)