meta2counts: Convert a manta object's meta slot data into counts
In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description Usage Arguments Value See Also Examples

This is a helper function for the mantaMethod

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

`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

a count matrix

manta, mantaMethod

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')