marray: Microarray array

In aaronwolen/mimager: mimager: The Microarray Imager

Description

Convert S4 microarray data structures into a three-dimensional array of matrices, where each matrix corresponds to an individual sample's microarray with values arranged to reflect the physical position of the corresponding feature (i.e., probe) on the microarray surface.

Usage

marray(object, type = NULL, select = NULL, transpose = NULL)

## S4 method for signature 'AffyBatch'
marray(object, type = "pm", select = NULL, transpose = FALSE)

## S4 method for signature 'PLMset'
marray(object, type = "residuals", select = NULL, transpose = FALSE)

## S4 method for signature 'FeatureSet'
marray(object, type = "pm", select = NULL, transpose = FALSE)

## S4 method for signature 'oligoPLM'
marray(object, type = "residuals", select = NULL, transpose = FALSE)

Arguments

object	a valid Bioconductor microarray data structure
type	for microarray objects type refers to probe type; for objects containing probe-level models (e.g., PLMsets) type refers to the value type (i.e, "residuals" or "weights"). See probe type section for more information.
select	a numeric, character or logical vector indicating samples to include
transpose	TRUE (the default), ensures the reconstructed microarrays are vertically oriented, as is typically expected. Set to FALSE to return an array in the orientation strictly specified by the platform coordinates

Value

three-dimensional array

Probe types

For microarray data structures the type argument determines the type of probe that should be included. The following table provides a list of valid values for each supported microarray class:

AffyBatch	"all"	"pm"	"mm"	-
ExpressionFeatureSet	"all"	"pm"	"mm"	-
GeneFeatureSet	"all"	"pm"	-	"bg"
ExonFeatureSet	"all"	"pm"	"mm"	"bg"
SnpFeatureSet	"all"	"pm"	"mm"	-

Examples

if (require(affydata, quietly = TRUE)) {
  data("Dilution", package = "affydata")
  dilution.array <- marray(Dilution, select = c("20A", "10A"))
}

aaronwolen/mimager documentation built on Dec. 9, 2019, 9:57 p.m.