otuSummary (version 0.1.2)

otuqiime: OTU table generated from 8 lakes over 4 years

Description

A data set containing bacterial counts from the North Temperate Lakes Microbial Observatory, the taxonomy column is in format generated by software platfor 'QIIME' (Caporaso et al 2010). The data set is published in Msphere (Linz et al 2017).

Usage

data("otuqiime")

Format

A data frame with 454 columns (453 samples plus 1 taxonomy) and 591 rows (OTUs).

Details

The first two letters of sample names denote the sampling site (e.g. "CB"), followed with epilimnion or hypolimnion ("E" or "H") and sampling date ("01OCT07"). The original data set have replicates ("R1" and "R2"), this data set only extracted the subset of "R2" (with extension ".R2" in sample names).

References

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336. Linz AM, Crary BC, Shade A, Owens S, Gilbert JA, Knight R et al (2017). Bacterial community composition and dynamics spanning five years in freshwater bog lakes. Msphere 2: e00169-00117.

Examples

data(otuqiime)
dim(otuqiime)
names(otuqiime)[1:10]
rownames(otuqiime)[1:10]
head(otuqiime$taxonomy)