manta {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.

### See Also

DGEList

### 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)

[Package manta version 1.26.0 Index]