Usage
caseof2Rs0G(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. The channel image data (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 despeckled.
ImgLimits
Integer. It instructs the algorithm to find spots in the specified central image area.
For example, for a 512 x 512 image with cutSides = 50, it will search for spots in the central area
[cutSides:(512-ImgLimits),ImgLimits:(512-ImgLimits)] of the image matrix.
BFarea
Integer. Defines a rectangular pseudo-spot size whose fluorescence will be estimated. This is
mainly used in BF image modeling where a fluorescence spot could not be originally detected. The value of
this parameter is also used as a cut-off to find matched spots across channel of the same sample image.
chip.type
Character string. It specifies the type of Fluidigm chip to be analyzed.
separator
Character string. Removes the Bright Field ("BF") and channel indicators (IDs) from the
image file names.
image.type
Character string. A triplet of IDs to characterize the type of images under study.
show.possible.contamination
Logical. If TRUE it reports all identified unmatched spots in both channels.