depth_filt: Sequencing depth filtering

In hilldiv: Integral Analysis of Diversity Based on Hill Numbers

Description

Filter samples based on a minimum sequencing depth.

Usage

depth_filt(countable, threshold)

Arguments

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.

Details

Sequencing depth filtering

Author(s)

Antton Alberdi, [e-mail]

References

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.

See Also

depth_cov, copy_filt

Examples

data(bat.diet.otutable)
depth_filt(bat.diet.otutable,5000)
depth_filt(bat.diet.otutable,threshold=20000)

hilldiv documentation built on Oct. 1, 2019, 5:04 p.m.