manta (version 1.18.0)

manta: 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)