subsetSamples: Filter results by sample

In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

Filter results by sample

Description

Create a SQM or SQMlite object containing only samples specified by the user, and the ORFs, contigs, bins, taxa and functions present in those samples.

Usage

subsetSamples(SQM, samples, remove_missing = TRUE, new_sample_names = NULL)

Arguments

SQM	SQM or SQMlite object to be subsetted.
samples	character. Samples to be included in the subset.
remove_missing	bool. If TRUE, ORFs, contigs, bins, taxa and functions absent from the selected samples will be removed from the subsetted object (default TRUE).
new_sample_names	character. New sample names to be included in the subset (default NULL).

Value

SQM or SQMlite object containing only the requested samples.

See Also

subsetTax, subsetFun, subsetORFs, combineSQM. The most abundant items of a particular table contained in a SQM object can be selected with mostAbundant.

SQMtools documentation built on Aug. 27, 2026, 9:07 a.m.