knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
metagenomeFeaturesand associated annotation packages can be used to obtain phylogentic trees, and representative sequences for 16S rRNA marker gene sequences when closed reference clustering is used.
metagenomeFeaturesand the Greengenes 16S rRNA database version 13.8 85\% OTUs to obtain a phylogenetic tree and representative sequences for XYZ study obtained from QIITA.
The gg 13.8 85% OTU is provided as part of the
library(metagenomeFeatures) gg85 <- get_gg13.8_85MgDb()
gg85 is a
MgDb class object with the taxonomic heirarchy, sequence data, and phylogeny for the Greengenes database clustered at the 0.85 similarity threshold.
For this vignette we are using 16S rRNA data from Rousk et al. 2010, a soil microbiome study, https://qiita.ucsd.edu/study/description/94. A BIOM and qiime mapping file for the study can be obtained from QIITA. A vector of Greengenes for the study cluster centers is included in this package for use in this vignette.
data_dir <- system.file("extdata", package = "metagenomeFeatures") soil_gg_ids <- readRDS(file.path(data_dir, "qiita_study_94_gg_ids.RDS"))
soil_mgF <- annotateFeatures(gg85, soil_gg_ids)
mgFeatures class object has the taxonomic heirarchy, phylogeny, and sequence data for the study OTUs.
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