manta: Create a MANTA object
In armbrustlab/manta: Microbial Assemblage Normalized Transcript Analysis

Description Usage Arguments Value See Also Examples

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.

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

`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

A MANTA object.

DGEList

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)