BASHExtended {beadarray} | R Documentation

## BASH - Extended Defect Analysis

### Description

Returns a score, which assesses the extent to which the background is changing across the array/strip.

### Usage

    BASHExtended(BLData, array, transFun = logGreenChannelTransform, neighbours = NULL, useLocs = TRUE, E = NULL, E.BG = NULL)

### Arguments

`BLData` | `BeadLevelList`
`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 `generateNeighbours` settings.
`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 `generateE` (with `bgfilter = "none"`, i.e. no background filter applied).
`E.BG` | Numerical vector - The background error image to use. Optional - if left blank, it will be computed from `E`, using default `BGFilter` settings (i.e. `method = "median"`).

### Details

`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

### Value

Scalar (Extended defect score)

### Author(s)

Jonathan Cairns

### References

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)

### See Also

`BASH`, `generateNeighbours`,

### Examples

    ## Not run:

    if(require(beadarrayExampleData)){

     data(exampleBLData)
     extended <- BASHExtended(exampleBLData, 1)

    }

    ## End(Not run)

[Package beadarray version 2.32.0 Index]