SpotPosition: Class representing spot positions
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Fields and Methods Author(s)

Package: aroma
Class SpotPosition

Object
~~|
~~+--SpotPosition

Directly known subclasses:

public static class SpotPosition
extends Object

A SpotPosition object contains physical (spatial) coordinates (in units of pixels) of the spots on a microarray slide.

1	SpotPosition(x=NULL, y=NULL)

`x`	An NxM `matrix` with x positions, where N is the number of spots on each slide and M is the number of slides. Alternatively, another SpotPosition object can be given and then argument `y` is ignored.
`y`	An NxM `matrix` with y positions of the same dimension as argument `x`.

Methods:

	`as.character`	Gets a character represenation of the spot positions.
	`as.data.frame`	Gets a data frame represenation of the spot positions.
	`equals`	-
	`extract`	-
	`getAspectRatio`	Gets the aspect ratio of the spots.
	`getBottomEdge`	Gets the y-coordinate of the spot at the very bottom.
	`getDistancesTo`	Gets the Euclidean distance from one spot to a set of other spots.
	`getLeftEdge`	Gets the x-coordinate of the left most spot.
	`getMaxHeight`	Gets the maximum y-distance between two spots.
	`getMaxWidth`	Gets the maximum x-distance between two spots.
	`getRightEdge`	Gets the x-coordinate of the right most spot.
	`getTopEdge`	Gets the y-coordinate of the spot at the very top.
	`nbrOfSlides`	Gets the number of slides.
	`nbrOfSpots`	Gets the number of spots in each of the slides.
	`plot`	Plots the spot positions in an xy scatter plot.
	`points`	Adds spot positions to an existing plot.
	`size`	Gets the number of spots in all slides together.
	`write`	Write a SpotPosition object to file.

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

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

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