compositional bias test

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

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')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(manta)
Loading required package: edgeR
Loading required package: limma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/manta/compbiasTest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compbiasTest
> ### Title: compositional bias test
> ### Aliases: compbiasTest
> 
> ### ** Examples
> 
> 
> manta.path <- system.file("extdata","PapaGO-BLAST.results-diatoms.Rdata", package="manta")
> load(manta.path)
> 			
> compbiasTest(x, meta.lev='genus_sp')
Analysis of Variance Table

Response: R
            Df Sum Sq Mean Sq F value    Pr(>F)    
subtaxa      6   98.4  16.394   6.576 6.538e-07 ***
Residuals 2710 6756.0   2.493                      
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>