beadarrayMSV (version 1.0.3)

getNormInd: Retrieve sub-bead pool indexes

Description

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

Usage

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

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

See Also

preprocessBeadSet, getNoiseDistributions

Examples

#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))