Description Usage Arguments Details Author(s) References See Also Examples
Filter samples based on a minimum sequencing depth.
1 | depth_filt(countable, threshold)
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countable |
An OTU table (matrix/data.frame) indicating the absolute OTU abundances of multiple samples. Columns must refer to samples and rows to OTUs. |
threshold |
A number indicating the minimum sequencing depth required to keep the sample. |
Sequencing depth filtering
Antton Alberdi, anttonalberdi@gmail.com
Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. 2019. Promises and pitfalls of using high-throughput sequencing for diet analysis. Molecular Ecology Resources, 19(2), 327-348.
1 2 3 | data(bat.diet.otutable)
depth_filt(bat.diet.otutable,5000)
depth_filt(bat.diet.otutable,threshold=20000)
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