## ---- vignettesetup，echo = false，message = false，警告= false -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ biocmanager”））install.packages（“ biocmanager”）＃biocmanager :: instart（“ panther.db”）## ---------------------------------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ AnnotationHub”））Biocmanager :: install（“ AnnotationHub”）＃library（AnnotationHub）＃ah <-AnnotationHub（）＃query（ah ah，“，” Panther。db“）[[1]] ## ----------- eval = true，messages = false，警告= false ---------------------------------------------------------------------------------------------------------------库（panther.db）## --------------------------------------------------------------------------------------------------------------------------------------------------------------＃help（“ panther.db”）## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- eval = true ------------------------------------------------------------------------------------------------------------- pthormenisms（Panther.db）< - “人” panther.db resetpthormenism（panther.db）豹.db ## -------------------------------------------------------------------------------------------------------------------------------------------------------- columns(PANTHER.db) ## ---- eval = TRUE-------------------------------------------------------------------------------------------------panther.db）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- head（键（panther.db，keytype =“ goslim_id”））go_ids ## ----------------= 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()