Array2Matrix {DECIPHER} | R Documentation

## Create a Matrix Representation of a Microarray

### Description

Converts the output of `DesignArray` into the sparse matrix format used by `NNLS`.

### Usage

    Array2Matrix(probes,
                 verbose = TRUE)

### Arguments

`probes` | A set of microarray probes in the format output by `DesignArray`.
`verbose` | Logical indicating whether to display progress.

### Details

A microarray can be represented by a matrix of hybridization efficiencies, where the rows represent each of the probes and the columns represent each the possible templates. This matrix is sparse since microarray probes are designed to only target a small subset of the possible templates.

### Value

A list specifying the hybridization efficiency of each probe to its potential templates.

`i` | Element's row index in the sparse matrix.
`j` | Element's column index in the sparse matrix.
`x` | Non-zero elements' values representing hybridization efficiencies.
`dimnames` | A list of two components: the names of each probe, and the names of each template.

### Author(s)

Erik Wright eswright@pitt.edu

### References

ES Wright et al. (2013) Identification of Bacterial and Archaeal Communities From Source to Tap. Water Research Foundation, Denver, CO.

DR Noguera, et al. (2014). Mathematical tools to optimize the design of oligonucleotide probes and primers. Applied Microbiology and Biotechnology. doi:10.1007/s00253-014-6165-x.

### See Also

`DesignArray`, `NNLS`

### Examples

    fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER")
    dna <- readDNAStringSet(fas)
    names(dna) <- 1:length(dna)
    probes <- DesignArray(dna)
    A <- Array2Matrix(probes)

[Package DECIPHER version 2.8.1 Index]