## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(HDO.db) ## ----------------------------------------------------------------------------- library(AnnotationDbi) ## ----------------------------------------------------------------------------- ls("package:HDO.db") packageVersion("HDO.db") ## ----------------------------------------------------------------------------- toTable(HDOmetadata) HDOMAPCOUNTS ## ----------------------------------------------------------------------------- doterm <- toTable(HDOTERM) head(doterm) ## ----------------------------------------------------------------------------- dotermlist <- as.list(HDOTERM) head(dotermlist) ## ----------------------------------------------------------------------------- doalias <- as.list(HDOALIAS) doalias[['DOID:0001816']] ## ----------------------------------------------------------------------------- dosynonym <- as.list(HDOSYNONYM) dosynonym[['DOID:0001816']] ## ----------------------------------------------------------------------------- anc_table <- toTable(HDOANCESTOR) head(anc_table) ## ----------------------------------------------------------------------------- anc_list <- AnnotationDbi::as.list(HDOANCESTOR) anc_list[["DOID:0001816"]] ## ----------------------------------------------------------------------------- parent_table <- toTable(HDOPARENTS) head(parent_table) ## ----------------------------------------------------------------------------- parent_list <- AnnotationDbi::as.list(HDOPARENTS) parent_list[["DOID:0001816"]] ## ----------------------------------------------------------------------------- off_list <- AnnotationDbi::as.list(HDO.db::HDOOFFSPRING) off_list[["DOID:0001816"]] ## ----------------------------------------------------------------------------- child_list <- AnnotationDbi::as.list(HDO.db::HDOCHILDREN) child_list[["DOID:4"]] ## ----------------------------------------------------------------------------- columns(HDO.db) ## use doid keys dokeys <- head(keys(HDO.db)) res <- select(x = HDO.db, keys = dokeys, keytype = "doid", columns = c("offspring", "term", "parent")) head(res) ## use term keys dokeys <- head(keys(HDO.db, keytype = "term")) res <- select(x = HDO.db, keys = dokeys, keytype = "term", columns = c("offspring", "doid", "parent")) head(res) ## ----------------------------------------------------------------------------- sessionInfo()