spotgrid {spotSegmentation} | R Documentation |
Determines row or column delimiters for spot locations from blocks of microarray slide image data.
spotgrid(chan1, chan2, rows = NULL, cols = NULL, span = NULL, show = FALSE)
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. |
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.
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.
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)