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)