otumothur: OTU table generated from 8 lakes over 4 years

In otuSummary: Summarizing OTU Table Regarding the Composition, Abundance and Beta Diversity of Abundant and Rare Biospheres

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 mothur format. The data set is published in Msphere (Linz et al, 2017). The data set is identical to otuqiime except for the taxonomy column in qiime format.

Usage

data("otumothur")

Format

A data frame with 454 columns (453 samples plus 1 taxonomy) and 591 rows (OTUs). The taxonomy is given in mothur format, with hierarchical taxonomy from kingdom to species separated with semiclone.

Details

The full version of the data set is published in Msphere (Linz et al 2017). 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). The data set is identical to otuqiime except that the taxonomy is in format generated by software 'mothur' (Schloss et al 2009).

Source

see the entire dataset at https://github.com/cran/OTUtable/tree/master/data

References

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. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.

Examples

data(otumothur)
dim(otumothur)
sapply(otumothur, class)
head(otumothur$taxonomy)

otuSummary documentation built on Sept. 8, 2023, 6:05 p.m.