HULKResids {beadarray}R Documentation

HULK - Residuals

Description

Calculates an set of weighted average residuals, one for each probe, based on the residuals of the surrounding probes.

Usage

HULKResids(BLData, array, neighbours = NULL, invasions = 20, what = "G")

Arguments

BLData BeadLevelList
array integer specifying which strip/array to plot
neighbours A Neighbours matrix. Optional - if left NULL, it will be computed.
invasions Integer - Number of invasions used when identifying neighbouring beads.
what Specify the data in the BLData to create the residuals from. Defaults to the foreground intensities of the green channel.

Details

HULKResids calculates a weighted average residual for each probe on the specified array of BLData. It makes use of the same neighbourhood calculations as other BASH functions. The average residuals are calculated as the sum of the residuals for each bead in the neighbourhood, divided by 1 plus the number of invasions it took to reach that bead. It is intended that HULKResids be called through HULK, but it is quite possible to call it as a stand alone function.

Value

A vector containing an average residual for each bead on the specified array of BLData.

Author(s)

Mike Smith

References

Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. (2008). BASH: a tool for managing BeadArray spatial artefacts. Bioinformatics, 24(24):2921-2.

See Also

HULK, BASH

Examples

data(BLData)
o <- HULKResids(BLData, 1)

[Package beadarray version 1.12.1 Index]