SpotStats {CONFESS} | R Documentation

## spotStats

### Description

It produces a table of estimated spot locations and fluorescence signals accompanied by informative plots. It can process the results of either spotCoords() for fluorescence-based estimation or forceBF() for BF image modelling estimation.

### 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 <<separator2>> 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.

### Value

A table of location and fluorescence estimated with accompanied plots

[Package CONFESS version 1.10.1 Index]