spotgrid: Gridding for Blocks of Microarray Spots

In spotSegmentation: Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots

Description

Determines row or column delimiters for spot locations from blocks of microarray slide image data.

Usage

spotgrid(chan1, chan2, rows = NULL, cols = NULL, span = NULL,
                 show = FALSE)

Arguments

chan1	matrix of pixel intensities from the first channel.
chan2	matrix of pixel intensities from the second channel.
rows	number of spots in a row of the image block.
cols	number of spots in a column of the image block.
span	Window size for locating peak signals. This can be of length 2, in which case the first value is interpreted as a window size for the rows and the second as a window size for the columns. A default is estimated from the image dimension and number of spots.
show	logical variable indicating whether or not to display the gridding result.

Value

A list with two elements, rowcut and colcut giving delimiters for the row and/or column gridding of the slide. The indexes indicate the start of a segment of the grid, except for the last one, which indicates the end of the grid.

References

Q. Li, C. Fraley, R. Bumgarner, K. Y. Yeung, and A. Raftery\ Robust model-based segmentation of microarray images,\ Technical Report No.~473, Department of Statistics, University of Washington, January 2005.

See Also

spotseg

Examples

data(spotSegTest)

# columns of spotSegTest:
#  1 intensities from the Cy3 (green) channel
#  2 intensities from the Cy5 (red) channel

dataTransformation <- function(x) (256*256-1-x)^2*4.71542407E-05 

chan1 <- matrix(dataTransformation(spotSegTest[,1]), 144, 199)
chan2 <- matrix(dataTransformation(spotSegTest[,2]), 144, 199)

Grid <- spotgrid( chan1, chan2, rows = 4, cols = 6, show = TRUE)

Example output

Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.

spotSegmentation documentation built on April 28, 2020, 9:18 p.m.