beadRegistrationData-class {beadarray} | R Documentation

## Class "beadRegistrationData"

### Description

A class for storing information relating to the registration of the image.

### Slots/List Components

Objects of this class contain the following slots

`layout`: | A list entry containing details of the structure of a BeadChip. By default entries for the number of sections, the number of segments per section and a logical value stating whether the chip is two colour are created.
`registrationData`: | A list with length equal to the total number of segments registered. Each entry contains a vector of the differences between the within bead-type variances calculated using randomly assigned bead IDs and those calculated using the provided bead IDs.
`coordinateData`: | A list with length equal to the total number of segments registered. Each entry contains the coordinates of the beads assigned to the segment, taken from the .locs file.
`cornerData`: | A list with length equal to the total number of segments registered. Each entry contains a set of four coordinate pairs that mark the corners of the segment within it's image. These can be extracted from the `coordinateData` and this slot may be removed at a later date.
`p95`: | A numeric vector storing the 95th percentile of bead intensities within each segment.
`imageLocations`: | Character vector storing the location of the tiff images of the array. These are obtained from the sectionData slot of the `beadLevelData` object that was processed by `checkRegistration`, and are required for visualising the bead locations.
`metrics`: | A data.frame, where each line contains the appropriate entry from the Metrics.txt file. Currently not used, but may be later.

### Methods

boxplot(regScores, plotP95 = FALSE)

### Author(s)

Mike Smith

### See Also

`checkRegistration`

[Package beadarray version 2.40.0 Index]