caseof1R1G {CONFESS} | R Documentation

## caseof1R1G

### Description

It processes the case of 1 spot in both channels. BF image modelling is not necessarily performed. It reports possible contamination.

### Usage

    caseof1R1G(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.

### Value

A list of location estimates

[Package CONFESS version 1.16.0 Index]