Retrieve Feature Data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Overview

Greengenes 13.8 85\% OTU MgDb

The gg 13.8 85% OTU is provided as part of the metagenomeFeatures package.

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.

gg85

QIITA Dataset

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"))

Obtaining Sequences and Phylogenetic Tree

soil_mgF <- annotateFeatures(gg85, soil_gg_ids)

The resulting mgFeatures class object has the taxonomic heirarchy, phylogeny, and sequence data for the study OTUs.

soil_mgF

Sequence data

mgF_seq(soil_mgF)

Tree data

mgF_tree(soil_mgF)


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metagenomeFeatures documentation built on May 2, 2018, 4:13 a.m.