hilldiv (version 1.5.1)

depth_filt: 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

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

# NOT RUN {
data(bat.diet.otutable)
depth_filt(bat.diet.otutable,5000)
depth_filt(bat.diet.otutable,threshold=20000)
# }