BGFilterWeighted {beadarray}R Documentation

Weighted Background Filter

Description

Finds local weighted means at each bead.

Usage

BGFilterWeighted(E = NULL, neighbours, invasions = 20, weights = NULL)

Arguments

E Error Image
neighbours A Neighbours matrix. Required.
invasions Integer - Number of invasions. This argument is passed to the function BGfilter.
weights Numerical vector - A vector of weights, from 0 to 1, to consider in the analysis. (see below.)

Details

This function finds the weighted mean of local bead intensities, using intensities from the given error image.

To obtain our weighted mean for each bead, we use an invasion process. Links between beads are defined in the neighbours matrix. We define the local beads as those which can be reached in invasions steps from the first bead, and then collect their error values.

We take a weighted mean of these error values, where the weights are calculated by taking the product of: a) 1/(the number of steps required to get to the bead from the central bead) b) (if supplied) the weights defined through the weights parameter.

This weighted mean is then assigned to the central bead.

Value

A vector - the weighted means. (NB: Whilst BGFilter manipulates the error image and returns an updated error image, e.g. subtracting the local median, this function does not - it merely returns the local weighted means.)

Author(s)

Jonathan Cairns

See Also

BGFilter

Examples

data(BLData)
E <- generateE(BLData,1,method = "mean")
neighbours <- generateNeighbours(BLData,1)
##bgf <- BGFilterWeighted(E, neighbours)

[Package beadarray version 1.10.0 Index]