image.RGList {Ringo}R Documentation

Function to visualize spatial distribution of raw intensities

Description

Function to visualize spatial distribution of raw intensities on NimbleGen Oligoarrays. Requires RGList with component genes complete with genes$X and genes$X coordinates of probes on array. arrayImage is a synonym of image.RGList.

Usage

## S3 method for class 'RGList':
image(x,arrayno,channel=c("red","green","logratio"),
         mycols=NULL, mybreaks=NULL,...)

Arguments

x object of class RGList containing red and green channel raw intensities; possibly result of readNimblegen.
arrayno integer; which array to plot; one of 1:ncol(x$R)
channel character; which channel to plot, either red, green or the logratio log2(red)-log2(green)
mycols vector of colors to use for image; if NULL defaults to colorRampPalette(c("White", "Yellow", "Red"))(10)
mybreaks optional numeric vector of breaks to use as argument breaks in image.default; default NULL means take length(mycols)+1 quantiles of the data as breaks.
... further arguments passed on to image.default

Value

invisibly returns matrix of raw intensities, in which rows and columns correspond to X and Y coordiantes on arrays. Can be directly plotted with function image.default.

Author(s)

Joern Toedling toedling@ebi.ac.uk

See Also

readNimblegen,image

Examples

   exDir <- system.file("exData",package="Ringo")
   exRG <- readNimblegen("example_files.txt","spottypes.txt",path=exDir)
   image(exRG,arrayno=1,channel="red")
   ## this example looks strange because the example data files only
   ## includes the probe intensities of probes mapped to chromosome 8.
   ## you can see these probes are distributed all over the array

[Package Ringo version 1.0.0 Index]