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Last data update: 2014.03.03

R: Create a MANTA object

manta

R Documentation

Create a MANTA object

Description

The MANTA object contains counts, genes, library information just like a EdgeR's DGEList. Additionally, however, it contains 'meta' annotation (typically taxinomic classifications). This function converts all of listed component elements into a MANTA object.

Usage

manta(counts, samples=makeSampleDF(counts), genes=NULL, meta=NULL, meta.sum=NULL, weights=NULL, norm=TRUE, disp=TRUE, ...)

Arguments

`counts`	A numeric matrix containing the read counts. Rows should be named by a unique gene identifier.
`samples`	The experimental sample dataframe (nearly identical to the one in a DGEList object).
`weights`	A numberic matrix of count weights for each count. Should be the same dimentions as the count table.
`genes`	A dataframe of genes annotations that have corresponding count data.
`meta`	A taxinomic level list of gene lists of cross tabulations of taxinomic (meta) annotations for genes that have corresponding count data.
`meta.sum`	A list of aggregated counts for (one per taxinomic level).
`norm`	boolean specifiying if manta should automatically normalize using calcNormFactors().
`disp`	boolean specifying if manta should automatically estimate the common dispersion via estimateCommonDisp().
`...`	additional parameters passed to DGEList

Value

A MANTA object.

Examples


cts.path <- system.file("extdata","PapaGO-BWA.counts-diatoms.tab", package="manta")
cts <- read.delim(cts.path)
samples <- makeSampleDF(cts)

x <- manta(counts= cts, samples = samples)

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/manta.Rd_%03d_medium.png", width=480, height=480)
> ### Name: manta
> ### Title: Create a MANTA object
> ### Aliases: manta
> 
> ### ** Examples
> 
> 
> cts.path <- system.file("extdata","PapaGO-BWA.counts-diatoms.tab", package="manta")
> cts <- read.delim(cts.path)
> samples <- makeSampleDF(cts)
> 
> x <- manta(counts= cts, samples = samples)
Warning message:
In estimateCommonDisp.DGEList(obj) :
  There is no replication, setting dispersion to NA.
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>