depth_filt {hilldiv}

Sequencing depth filtering

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)