| nice_tidy {ulrb} | R Documentation |
V4-V5 16S rRNA gene amplicons, clean OTU table in tidy/long format (N-ICE, 2015)
Description
Original OTU table (nice) in "long" format.
Usage
nice_tidy
Format
nice_tidy
A data frame with 4716 rows and 10 columns:
- Sample
Sample ID
- Abundance
Abundance
- OTU
OTU ID
- Domain
Domain level classification of OTU
- Phylum
Domain level classification of OTU
- Class
Domain level classification of OTU
- Order
Domain level classification of OTU
- Family
Domain level classification of OTU
- Genus
Domain level classification of OTU
- Species
Domain level classification of OTU
...
Details
A new column (Sample) includes the sample identifiers and a new column (Abundance) includes the abundance for each OTU. For details on OTU table processing see help pages for nice and nice_raw.
Some details on N-ICE dataset:
This dataset resulted from the Norwegian Young Sea Ice expedition (N-ICE) in 2015 (Granskog et al., 2018). The sample processing and DNA sequencing were described in de Sousa et al., 2019, the bioinformatic processing was performed by the MGnify platform (v5) (Mitchell et al., 2020).
Since the purpose of this dataset if for creating examples and testing the package, we did not apply strict quality control to the final OTU table. Thus, we didn't remove singletons, etc. However, we did remove any non-prokarotic OTUs and organelles, if any (Pascoal et al., 2022).
Source
https://www.ebi.ac.uk/metagenomics/studies/MGYS00001922#analysis
References
Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., Sakharova, E., Scheremetjew, M., Korobeynikov, A., Shlemov, A., Kunyavskaya, O., Lapidus, A., & Finn, R. D. (2019). MGnify: the microbiome analysis resource in 2020. Nucleic Acids Research, 48(D1), D570–D578.
Granskog, M. A., Fer, I., Rinke, A., & Steen, H. (2018). Atmosphere-Ice-Ocean-Ecosystem Processes in a Thinner Arctic Sea Ice Regime: The Norwegian Young Sea ICE (N-ICE2015) Expedition. Journal of Geophysical Research: Oceans, 123(3), 1586–1594.
de Sousa, A. G. G., Tomasino, M. P., Duarte, P., Fernández-Méndez, M., Assmy, P., Ribeiro, H., Surkont, J., Leite, R. B., Pereira-Leal, J. B., Torgo, L., & Magalhães, C. (2019). Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. Microbial Ecology, 78(2), 388–408.
Pascoal, F., Costa, R., Assmy, P., Duarte, P., & Magalhães, C. (2022). Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies. Microbial Ecology, 84(1), 59–72.