SongQAData: Obtain the Song quality assurance dataset

In microbiome/microbiomeDataSets: Experiment Hub based microbiome datasets

Obtain the Song quality assurance dataset

Description

Obtain the microbiome data from Song et al. (2016).

Usage

SongQAData()

qa10934()

Details

The SongQA dataset contains microbiome data from a study comparing different sample preparation methods focusing on temperature and DNA extraction methods mainly.

The dataset was generated by sequencing the variable region 4 of 16S rRNA genes via Illumina HiSeq or MiSeq.

Column metadata was reconstructed from sample names and includes information on the source, timepoint, extraction method, temperature conditions and other optional data.

Row metadata contains taxonomic information on the Phylum, Family and Genus level.

All data are downloaded from ExperimentHub and cached for local re-use.

Value

a TreeSummarizedExperiment

Author(s)

Felix G.M. Ernst

Source

https://qiita.ucsd.edu/study/description/10394

References

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. Se Jin Song, Amnon Amir, Jessica L. Metcalf, Katherine R. Amato, Zhenjiang Zech Xu, Greg Humphrey, Rob Knight. mSystems May 2016, 1 (3) e00021-16; DOI: 10.1128/mSystems.00021-16

Examples

tse <- SongQAData()

microbiome/microbiomeDataSets documentation built on July 31, 2022, 6:09 a.m.