meta2counts {manta} | R Documentation

## 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

    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')

[Package manta version 1.32.0 Index]