topSpots.MAData: Gets the top spots

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

Description

Gets (approximately) the n spots with the highest M values, if n greater or equal to one, and the 100*n percentage if n is less than one.

Usage

## S3 method for class 'MAData'
topSpots(this, n=50, nbins=1, slide=1, include=NULL, exclude=NULL, limits=c("both", "upper", "lower"), X="A", Y="M", ...)

Author(s)

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

See Also

For more information see MAData.

Examples

  # The option 'dataset' is used to annotate plots.
  options(dataset="sma:MouseArray")

  SMA$loadData("mouse.data")
  layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
  raw <- RawData(mouse.data, layout=layout)
  ma <- getSignal(raw, bgSubtract=TRUE)
  normalizeWithinSlide(ma, "s")
  top100  <- topSpots(ma, 100);   # The top 100 spots
  top0.01 <- topSpots(ma, 0.01);  # The top 1 percent of the spots

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