| generateE {beadarray} | R Documentation |
Generates an Error Image from the data in a BeadLevelList object.
generateE(BLData, array, neighbours = NULL, log = TRUE, method = "median", what = "residG", bgfilter = "none", invasions = 20)
BLData |
BeadLevelList |
array |
integer specifying which strip/array to plot |
neighbours |
A Neighbours matrix. Optional - if left NULL, it will be computed. |
log |
Logical. If TRUE, compute residuals on the log scale. |
method |
Method for computing residuals. Options are "mean" and "median" |
what |
What to derive the error image from, as used in getArrayData. |
bgfilter |
Method passed to the function BGFilter. Options are "none", "mean", "median", "MAD" and "medianMAD". |
invasions |
Integer - Number of invasions. This argument is passed to the function BGfilter. |
generateE creates an error image, usually based on bead residuals. This output can then be fed into BASHDiffuse or BASHExtended.
If what is residG, residR, or residM, then residuals are calculated based on method. For other values of what, the residuals are not calculated.
We then apply a "background filter" to this data, using the function BGFilter with arguments bgfilter and invasions - see its help file for more details. The background filter subtracts an estimate of the local background of the error image, and/or scales by the local MAD. This step is disabled by using bgfilter = "none".
An "Error Image" - a vector of length equal to the number of beads on the array.
Jonathan Cairns
data(BLData) E <- generateE(BLData,1) E <- generateE(BLData,1, invasions = 10) #reduced no of invasions to increase speed. E <- generateE(BLData,1, bgfilter = "none") #residuals (median)