pplacer2manta: convert a pplacer taxinomic placement repository to a MANTA...
In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description Usage Arguments Value See Also Examples

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).

1
2
3

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

`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()

A MANTA object

manta, in2manta

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
 	     )