getSpotPosition.ScanAlyzeData: Gets physical positions of the spots

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Gets physical positions (in pixels) of the spots on one or several slides.

Usage

## S3 method for class 'ScanAlyzeData'
getSpotPosition(this, slides=NULL, index=NULL, ...)

Arguments

slides	Specifying which for slides the spot positions should be extracted. If NULL, all slides are considered.
index	The spots for which the position is returned. If NULL all spots are considered.

Details

The ScanAlyze software does not return the center position of a spot, but the TOP LEFT BOT and RIGHT coordinates. This method assumes that the center of the spot is in the center of this box.

Value

Returns a SpotPosition object containing the positions of the spots on the specified slides.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

For more information see ScanAlyzeData.

Examples

  sa <- ScanAlyzeData$read("group4.dat", path=system.file("data-ex", package="aroma"))

  # Gets the spot positions
  xy <- getSpotPosition(sa)

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.