beadarray (version 2.22.2)

BASHExtended: 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").

Value

Scalar (Extended defect score)

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

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)