manta (version 1.18.0)

pplacer2manta: 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
 	     )