## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) suppressPackageStartupMessages(library(metagenomeFeatures)) ## ----------------------------------------------------------------------------- library(metagenomeFeatures) gg85 <- get_gg13.8_85MgDb() ## ----------------------------------------------------------------------------- taxa_keytypes(gg85) taxa_columns(gg85) head(taxa_keys(gg85, keytype = c("Kingdom"))) ## ----------------------------------------------------------------------------- ## Only returns taxa mgDb_select(gg85, type = "taxa", keys = c("Vibrionaceae", "Enterobacteriaceae"), keytype = "Family") ## Only returns seq mgDb_select(gg85, type = "seq", keys = c("Vibrionaceae", "Enterobacteriaceae"), keytype = "Family") ## Returns taxa, seq, and tree mgDb_select(gg85, type = "all", keys = c("Vibrionaceae", "Enterobacteriaceae"), keytype = "Family") ## ----------------------------------------------------------------------------- ve_select <- mgDb_select(gg85, type = "all", keys = c("Vibrionaceae", "Enterobacteriaceae"), keytype = "Family") mgFeatures(taxa = ve_select$taxa, tree = ve_select$tree, seq = ve_select$seq, metadata = list("gg85 subset Vibrionaceae and Enterobacteriaceae Family")) ## ----------------------------------------------------------------------------- annotateFeatures(gg85, query = ve_select$taxa$Keys) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()