copy_filt {hilldiv}

OTU/ASV copy number filtering

Description

As DNA sequencing data include PCR and sequencing errors, copy number thresholds are commonly applied to discard the OTUs with low number of sequence copies. This threshold can be absolute or (ideally) relative to the sequencing depth of each sample.

Usage

copy_filt(abund, threshold)

Arguments

abund

A vector or a matrix/data.frame indicating the relative abundances of one or multiple samples, respectively. If a matrix/data.frame is provided, columns must refer to samples and rows to OTUs.

threshold

An integer or a decimal number indicating the cut-off threshold. If an integer is provided, an absolute threshold is used (same threshold for all samples). If a decimal number is provided a relative copy number threshold is applied (dependent on the sequencing depth of each sample).

Details

OTU/ASV copy number 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, tss

Examples

data(bat.diet.otutable)
#Remove singletons from all samples
copy_filt(bat.diet.otutable,2)
#Remove OTUs represented by less than 0.01% of the total reads per sample.
copy_filt(bat.diet.otutable,0.0001)