pplacer2manta {manta} | R Documentation

## convert a pplacer taxinomic placement repository to a MANTA object

### Description

This function creates a single manta object by traversing a directory of directories of pplacer SQLite taxonomy databases (where each database called "taxtable.db" resides in a sub folder named by a single gene locus).

### Usage

    pplacer2manta(dir, group.pattern='_([[:alpha:]]+)_',
     		groups=c('coastal','costal','DCM','surface','upwelling'),
    		uk.name='unknown', ...)

### Arguments

`dir` | directory of gene directories each with a single gene taxonomic read placement database.
`group.pattern` | the regular expression used to parse out the name of the different conditions/groups from the read names.
`groups` | the actual list of groups.
`uk.name` | the rowname to appear in each othe meta tabulation tables for the unplaceable reads.
`...` | additional parameters passed along to manta()

### Value

A MANTA object

### See Also

manta, in2manta

### Examples

    KOG.SQLite.repo <- system.file('extdata','pplacer',package='manta')
    pplacer2manta(dir=KOG.SQLite.repo,
     	      groups=c('coastal','costal','DCM','surface','upwelling'),
     	      norm=FALSE, disp=FALSE
     	     )

[Package manta version 1.26.0 Index]