meta2counts: Convert a manta object's meta slot data into counts

In manta: Microbial Assemblage Normalized Transcript Analysis

Description

This is a helper function for the mantaMethod

Usage

meta2counts(obj, meta.lev, rm.sum=TRUE, meta.subset=NULL)

Arguments

obj	A manta object.
meta.lev	The taxinomic rank level (phylum, genus, etc) from which to pull counts.
rm.sum	Whether or not to remove the overall 'sum' (over all conditions) column.
meta.subset	Which sub rank level (the subset) for which to estimate the normalization. By default is does the overall normalization

Value

a count matrix

See Also

manta, mantaMethod

Examples

manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
load(manta.path)

tab <- meta2counts(x, meta.lev='genus_sp', meta.subset='Pseudo-nitzschia granii')

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