readTIFF: Read the Illumina tiff images

Description

Reads Illumina tiff images and produces a matrix of pixel values.

Usage

readTIFF(fileName, path = NULL, verbose = FALSE, xlim = NULL, ylim = NULL)

Arguments

fileName

String specifying the name of the tiff image to be read.

path

String specifying the path to the desired image. The default value of NULL means the current working directory will be used.

verbose

If TRUE then details from the header of the tiff are printed as it is read. These include things like the byte order, the number of pixels in the image, the number of tags in the header etc. Defaults to FALSE as this is generally not of interest.

xlim

Used to specify a subsection of the image to read in. Takes a two entry vector e.g c(m,n) specifying that only pixels with x-coordinates between m and n (inclusive) should be read in.

ylim

Same a xlim, but for the y-cordinates.

Value

Returns a matrix with the same dimensions as the pixels in the tiff file to be read in.

Details

This function has been specifically written to read the grayscale tiff images which are produced by the Illumina scanners. It is not generic enough to read all tiff files, although this functionality may be added in the future.

Given that the raw images can be quite large, functionality has also been included to read tiffs that have been compressed as either .bz2 or .gz files. Identification is performed based on the file extension and it is assumed that each tif is compressed individually. Support for zip files may be added in the future.