## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- library("BiocStyle") ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager")) install.packages("BiocManager") # BiocManager::install("PANTHER.db") ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("AnnotationHub")) BiocManager::install("AnnotationHub") # library(AnnotationHub) # ah <- AnnotationHub() # query(ah, "PANTHER.db")[[1]] ## ----eval = TRUE, message=FALSE, warning=FALSE-------------------------------- library(PANTHER.db) ## ----eval = FALSE------------------------------------------------------------- # help("PANTHER.db") ## ----eval = TRUE-------------------------------------------------------------- PANTHER.db ## ----eval = TRUE-------------------------------------------------------------- availablePthOrganisms(PANTHER.db)[1:5,] ## ----eval = TRUE-------------------------------------------------------------- pthOrganisms(PANTHER.db) <- "HUMAN" PANTHER.db resetPthOrganisms(PANTHER.db) PANTHER.db ## ----eval = TRUE-------------------------------------------------------------- columns(PANTHER.db) ## ----eval = TRUE-------------------------------------------------------------- keytypes(PANTHER.db) ## ----eval = TRUE-------------------------------------------------------------- go_ids <- head(keys(PANTHER.db,keytype="GOSLIM_ID")) go_ids ## ----eval = TRUE-------------------------------------------------------------- cols <- "CLASS_ID" res <- mapIds(PANTHER.db, keys=go_ids, column=cols, keytype="GOSLIM_ID", multiVals="list") lengths(res) res_inner <- select(PANTHER.db, keys=go_ids, columns=cols, keytype="GOSLIM_ID") nrow(res_inner) tail(res_inner) ## ----eval = TRUE-------------------------------------------------------------- res_left <- select(PANTHER.db, keys=go_ids, columns=cols,keytype="GOSLIM_ID", jointype="left") nrow(res_left) tail(res_left) ## ----eval = TRUE-------------------------------------------------------------- term <- "PC00209" select(PANTHER.db,term, "CLASS_TERM","CLASS_ID") ancestors <- traverseClassTree(PANTHER.db,term,scope="ANCESTOR") select(PANTHER.db,ancestors, "CLASS_TERM","CLASS_ID") parents <- traverseClassTree(PANTHER.db,term,scope="PARENT") select(PANTHER.db,parents, "CLASS_TERM","CLASS_ID") children <- traverseClassTree(PANTHER.db,term,scope="CHILD") select(PANTHER.db,children, "CLASS_TERM","CLASS_ID") offspring <- traverseClassTree(PANTHER.db,term,scope="OFFSPRING") select(PANTHER.db,offspring, "CLASS_TERM","CLASS_ID") ## ----------------------------------------------------------------------------- sessionInfo()