Array2Matrix: Create a Matrix Representation of a Microarray

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

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 [e-mail]

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)

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.