getCsFAIL {CONFESS} | R Documentation

## getCsFAIL

### Description

A helper to re-estimate the spot location or find the capture site location (BF image modelling).

### Usage

    getCsFAIL(centerR, centerG, origImg, chaImgs, minDiff, despeckle,
      ImgLimits, BFarea, chip.type, separator, image.type)

### 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 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.
`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.
`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 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.

### Value

Location statistics under BF image modelling

[Package CONFESS version 1.14.0 Index]