class-beadRegistrationData: Class "beadRegistrationData"

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

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

markdunning/beadarray-devel documentation built on May 21, 2019, noon