getNormInd: Retrieve sub-bead pool indexes

Description Usage Arguments Value Note Author(s) See Also Examples

Description

Creates an array of logical indexes to each bead-type for use in normalization

Usage

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getNormInd(beadInfo, featureNames, normID = NULL, verbose = TRUE)

Arguments

beadInfo

Data-frame containg data on each marker in the experiment, specifically the “Address”, “Address2”, and “Norm.ID” connecting beads to markers (usually exported from Illumina's GenomeStudio Genotyping Module)

featureNames

Character vector with bead-type names (addresses)

normID

Character vector with one or more sub-bead pool indexes. If NULL, all Norm.ID's found in beadInfo are used

verbose

If TRUE, the sum of each sub-bead pool is printed

Value

Matrix of size (length(featureNames) x length(normID)), with logical indices to the sub-bead pool to which each bead-type belongs

Note

Beads manufactured in different pools should be normalised separately

Author(s)

Lars Gidskehaug

See Also

preprocessBeadSet, getNoiseDistributions

Examples

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## Not run: 
#Common use includes BeadSetIllumina-object
rPath <- system.file("extdata", package="beadarrayMSV")
BSDataRaw <- readBeadSummaryOutput(path=rPath,recursive=TRUE)
beadInfo <- read.table(paste(rPath,'beadData.txt',sep='/'),sep='\t',
    header=TRUE,as.is=TRUE)
rownames(beadInfo) <- make.names(beadInfo$Name)
normInd <- getNormInd(beadInfo,featureNames(BSDataRaw))

## End(Not run)


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