## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE------------------------ suppressPackageStartupMessages({ library(customCMPdb); library(ChemmineR) }) ## ----install, eval=FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("customCMPdb") ## ----inst_git, eval=FALSE----------------------------------------------------- # devtools::install_github("yduan004/customCMPdb", build_vignettes=TRUE) ## ----load, eval=TRUE, message=FALSE------------------------------------------- library(customCMPdb) library(help = "customCMPdb") # Lists package info ## ----load_vignette, eval=FALSE, message=FALSE--------------------------------- # browseVignettes("customCMPdb") # Opens vignette ## ----sql, eval=TRUE, message=FALSE-------------------------------------------- conn <- loadAnnot() library(RSQLite) dbListTables(conn) drugAgeAnnot <- dbReadTable(conn, "drugAgeAnnot") head(drugAgeAnnot) dbDisconnect(conn) ## ----da, eval=TRUE, message=FALSE, results=FALSE------------------------------ da_sdfset <- loadSDFwithName(source="DrugAge") ## ----da_chemmineR, eval=TRUE, message=FALSE, results=FALSE-------------------- ChemmineR::cid(da_sdfset) <- ChemmineR::sdfid(da_sdfset) ChemmineR::plot(da_sdfset[1]) ## ----db, eval=FALSE----------------------------------------------------------- # db_sdfset <- loadSDFwithName(source="DrugBank") ## ----cmap, eval=TRUE, message=FALSE, results=FALSE---------------------------- cmap_sdfset <- loadSDFwithName(source="CMAP2") ## ----lincs, eval=TRUE, message=FALSE, results=FALSE--------------------------- lincs_sdfset <- loadSDFwithName(source="LINCS") ## ----download_db, eval=TRUE, message=FALSE------------------------------------ library(AnnotationHub) ah <- AnnotationHub() annot_path <- ah[["AH79563"]] ## ----custom, eval=TRUE, message=FALSE, results=FALSE-------------------------- chembl_id <- c("CHEMBL1000309", "CHEMBL100014", "CHEMBL10", "CHEMBL100", "CHEMBL1000", NA) annot_tb <- data.frame(cmp_name=paste0("name", 1:6), chembl_id=chembl_id, feature1=paste0("f", 1:6), feature2=rnorm(6)) addCustomAnnot(annot_tb, annot_name="myCustom") ## ----del, eval=TRUE, message=FALSE-------------------------------------------- listAnnot() deleteAnnot("myCustom") listAnnot() ## ----default, eval=FALSE------------------------------------------------------ # defaultAnnot() ## ----query, eval=TRUE, message=FALSE------------------------------------------ query_id <- c("CHEMBL1064", "CHEMBL10", "CHEMBL113", "CHEMBL1004", "CHEMBL31574") listAnnot() qres <- queryAnnotDB(query_id, annot=c("drugAgeAnnot", "lincsAnnot")) qres # query the added custom annotation addCustomAnnot(annot_tb, annot_name="myCustom") qres2 <- queryAnnotDB(query_id, annot=c("lincsAnnot", "myCustom")) qres2 ## ----not_chembl, eval=TRUE, message=FALSE------------------------------------- query_id <- c("BRD-A00474148", "BRD-A00150179", "BRD-A00763758", "BRD-A00267231") qres3 <- queryAnnotDB(chembl_id=query_id, annot=c("lincsAnnot")) qres3 ## ----sessionInfo-------------------------------------------------------------- sessionInfo()