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

In manta: Microbial Assemblage Normalized Transcript Analysis

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

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

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

manta documentation built on Oct. 31, 2019, 3:03 a.m.