Usage
spotCoords(centerR, centerG, origImg, chaImgs, minDiff, despeckle, ImgLimits, BFarea, chip.type, separator, image.type, show.possible.contamination)
Arguments
centerR
Data matrix. The location statistics of one channel.
centerG
Data matrix. The location statistics of the other channel.
origImg
Data matrix. The original BF image to be read and processed.
chaImgs
List. A list of the red and green channel images (data matrices) of a sample
minDiff
Float. the mu_hat of the H0: image-to-noise ratio =
log(foreground_signal) - log(background_signal) = mu_hat. Rejection of H0
implies that the identified spot is brighter than background. Default is 0.5.
despeckle
Logical. If TRUE, the BF image is descpeckled.
ImgLimits
Integer. It instructs the algorithm to find spots in a certain central image area.
For example, for a 512 x 512 image with ImgLimits = 50, it will search for spots in
the central area [ImgLimits:(512-ImgLimits),ImgLimits:(512-ImgLimits)] of the image matrix.
BFarea
Integer. Defines a rectangular pseudo-spot size whose fluorescence will be estimated.
separator
Character string. Removes the Bright Field ("BF") and channel indicators from the
image file names.
image.type
Character string. A triplet of IDs to characterize the type of images under study.
They refer to the ImageType part of the original image or txt file names.
show.possible.contamination
Logical. If TRUE it reports all identified unmatched spots in both channels.
type
Character string. It specifies the type of Fluidigm chip to be analyzed.