meta2counts {manta} | R Documentation |
This is a helper function for the mantaMethod
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')