GlobalPatterns: GlobalPatterns

In microbiome/mia: Microbiome analysis

GlobalPatterns

Description

GlobalPatterns compared the microbial communities from 25 environmental samples and three known "mock communities" at a an average depth of 3.1 million reads per sample. Authors reproduced diversity patterns seen in many other published studies, while investigating technical bias by applying the same techniques to simulated microbial communities of known composition. Special thanks are given to J. Gregory Caporaso for providing the OTU-clustered data files for inclusion in the phyloseq package, from which this data was converted to TreeSummarizedExperiment.

Usage

data(GlobalPatterns)

Format

A TreeSummarizedExperiment with 19216 features and 26 samples. The rowData contains taxonomic information at Kingdom, Phylum, Class, Order, Family, Genus and Species levels. The colData includes:

X.SampleID

Sample ID taken from the corresponding study

Primer

primer used for sequencing

Final_Barcode

final barcode (6 nucleotides)

Barcode_truncated_plus_T

truncated barcode with an added tyrosine (6 nucleotides)

Barcode_full_length

complete barcode with a length of 11 nucleotides

SampleType

sampling type by collection site (Soil, Feces, Skin, Tongue, Freshwater, Creek Freshwater, Ocean, Estuary Sediment and Mock)

Description

additional information (sampling location, environmental factors and study type)

Author(s)

Caporaso, J. G., et al.

References

Caporaso, J. G., et al. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS, 108, 4516-4522. https://doi.org/10.1073/pnas.1000080107

See Also

mia-datasets

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.