BASHExtended: BASH - Extended Defect Analysis

In markdunning/beadarray-devel: Quality assessment and low-level analysis for Illumina BeadArray data

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)

markdunning/beadarray-devel documentation built on May 21, 2019, noon