generateE {beadarray}R Documentation

Generate Error Image for BeadLevelList object

Description

Generates an Error Image from the data in a BeadLevelList object.

Usage

generateE(BLData, array, neighbours = NULL, log = TRUE, method = "median", what = "residG", bgfilter = "none", invasions = 20)

Arguments

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.

Details

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".

Value

An "Error Image" - a vector of length equal to the number of beads on the array.

Author(s)

Jonathan Cairns

See Also

BGFilter

Examples

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)

[Package beadarray version 1.10.0 Index]