compbiasTest: compositional bias test

In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description

.

Usage

compbiasTest(x, pair=nv(levels(x$samples$group)[1:2] , c('ref','obs')), meta.lev='phylum',  meta.lev.lim=min(10,nrow(x$meta.sum[[meta.lev]])))

Arguments

x	a MANTA object.
pair	named vector of the pair of conditions of interest
meta.lev	which taxinomic level should this test be run at
meta.lev.lim	how many underlying taxinomic levels should the analysis be limited to

Value

A DGEList object.

See Also

DGEList, manta

Examples

manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
load(manta.path)
			
compbiasTest(x, meta.lev='genus_sp')

armbrustlab/manta documentation built on Dec. 17, 2019, 12:06 a.m.