Learn R Programming

manta (version 1.18.0)

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

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

Run this code


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')


Run the code above in your browser using DataLab