BASHExtended {beadarray} | R Documentation |
Returns a score, which assesses the extent to which the background is changing across the array/strip.
BASHExtended(BLData, array, transFun = logGreenChannelTransform, neighbours = NULL, useLocs = TRUE, E = NULL, E.BG = NULL)
BLData |
|
array |
integer specifying which section/array to analyse |
transFun |
Function to use to transform data prior to running BASH. |
neighbours |
A Neighbours matrix. Optional - if left NULL, it will be computed, using default |
useLocs |
Logical value, specifiying whether the .locs file (if present) should be used to determine neighbours. |
E |
Numerical vector - The error image to use. Optional - if left blank, it will be computed, using |
E.BG |
Numerical vector - The background error image to use. Optional - if left blank, it will be computed from |
BASHExtended
assesses the change of background across an array.
The error image used should not be background filtered (as opposed to the error image used in BASHDiffuse
). Here, E is the error image
Scalar (Extended defect score)
Jonathan Cairns
J. M. Cairns, M. J. Dunning, M. E. Ritchie, R. Russell, and A. G. Lynch (2008). BASH: a tool for managing BeadArray spatial artefacts. Bioinformatics 15; 24(24)
## Not run: if(require(beadarrayExampleData)){ data(exampleBLData) extended <- BASHExtended(exampleBLData, 1) } ## End(Not run)