pplacer2manta: convert a pplacer taxinomic placement repository to a MANTA...

Description Usage Arguments Value See Also Examples

View source: R/Pplacer.R

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

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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

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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
 	     )

manta documentation built on Oct. 31, 2019, 3:03 a.m.