Usage
SpotStats(img, chaImgs, binChaImgs, center, other.spots, BFcoords, BFarea, log.transform, warning, minDiff, separator, image.type)
Arguments
img
Data matrix. The original data of the BF image to be read and processed.
chaImgs
List. A list of the channel images (data matrices) of a sample.
binChaImgs
List. A list of binary segmented channel image data.
center
Data matrix. The 2-dimensional location of the spot's representative center.
BFcoords
List. A list of statistics describing the C1 chip line patterns (for BF image modelling).
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.
log.transform
Logical. If TRUE the image data are plotted in the log scale.
warning
Character string. An indicator of the estimation type that has been internally performed, i.e.
fluorescence-based or BF image modelling.
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.
separator
Character string. Removes the Bright Field ("BF") and channel indicators from the
image file names (see <> in readFiles()).
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.