metataxa2subcounts: create a new (sub) count table out of a subcomponent of the...

Description Usage Arguments Value See Also Examples

View source: R/Pplacer.R

Description

A simple and easy way to pull a subcomponent transcriptome out of the metatranscriptome. This one line function is useful for those wanting to just see the count data for one species or to create a new DGE or manta object on a subset of data.

Usage

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metataxa2subcounts(x, meta.lev='species', taxa.filter)

Arguments

x

a manta object.

meta.lev

the name of the taxinomic rank on which to subset.

taxa.filter

the name of the taxonomy at the meta.lev rank on which to subset.

Value

a count table

See Also

manta

Examples

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load(system.file('extdata','PapaGO-BLAST.results-diatoms.Rdata',package='manta'))
metataxa2subcounts(x, meta.lev='species', taxa.filter='Pseudo-nitzschia granii')

armbrustlab/manta documentation built on Dec. 17, 2019, 12:06 a.m.