createAlleleSet: Create AlleleSetIllumina or MultiSet objects

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

View source: R/beadarrayMSV.R

Description

An "AlleleSetIllumina" (or "MultiSet") object is created, either by transforming a "BeadSetIllumina" object into an "AlleleSetIllumina" object, by reading from text-files containing pre-processed data, or by merging existing objects

Usage

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createAlleleSet(BSData, beadInfo, normOpts, includeAB = FALSE)

createAlleleSetFromFiles(dataFiles, markers, arrays,
    phenoInfo = NULL, beadInfo = NULL, sep = "\t", quote = "")

createMultiSetFromFiles(dataFiles, markers, arrays,
    phenoInfo = NULL, beadInfo = NULL, sep = "\t", quote = "")

assignToAlleleSet(BSRed, BSAdd)

Arguments

BSData

"BeadSetIllumina" object

beadInfo

Data-frame containing an entry for each marker, and the columns “Name”, “SNP”, “ILMN.Strand”, “Address”, “Address2”, and “Norm.ID”, as exported from Illumina's GenomeStudio Genotyping Module (or relatives). May also contain columns relating to genotype calls (see callGenotypes)

normOpts

List containing at least the elements “dist” and “pNorm” (see setNormOptions)

includeAB

If TRUE, the Cartesian signal arrays “A” and “B” are returned as assayData entries in the new "AlleleSetIllumina" object

dataFiles

Character vector containing filenames where the different data-tables are saved (see makeFilenames)

markers

Index to markers in the dataFiles files

arrays

Index to arrays/samples in the dataFiles files

phenoInfo

Data-table with phenotype data. Argument is ignored if “phFile” is provided in dataFiles

sep

Field delimiter in text-files (see read.table)

quote

Quote-marks used for character strings (see read.table)

BSRed

"AlleleSetIllumina" object

BSAdd

"AlleleSetIllumina" object with data to include in BSRed

Details

A "BeadSetIllumina" object contains bead-type information, whereas an "AlleleSetIllumina" object contains marker information (for each Infinum I marker, there are two bead-types). The function createAlleleSet takes a "BeadSetIllumina" object as input and merges the “R” and “G” intensities into “A” and “B” intensities. The former relates to bead-types and the latter relates to markers as defined in beadInfo. The required polar coordinate intensities “intensity” and “theta” are estimated based on “A” and “B”, and depend on the distance measures defined in normOpts. The angles “theta” are scaled such that {0, 90} degrees are represented by {0, 1}, and “intensity” vs. “theta” for single markers are usually plotted on Cartesian axes for genotype calling.

If data-files are available for all required assayData, phenoData, and featureData elements, an "AlleleSetIllumina" or a "MultiSet" object may be constructed with create-AlleleSetFromFiles or createMultiSetFromFiles, respectively. The former has three required assayData elements whereas the latter has none.

Sometimes, and in particular after manual genotype calling, there is a need to update an "AlleleSetIllumina" object with new information. The function assignToAlleleSet adds any data in BSAdd to BSRed, overwriting previous data if there is a conflict

Value

Object of class "AlleleSetIllumina" or "MultiSet"

Author(s)

Lars Gidskehaug

See Also

AlleleSetIllumina, MultiSet, writeAlleleSet, makeFilenames

Examples

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## Not run: 
#Read raw data files into BeadSetIllumina object
rPath <- system.file("extdata", package="beadarrayMSV")
BSDataRaw <- readBeadSummaryOutput(path=rPath,recursive=TRUE)

#Find indexes to sub-bead pools
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))

#Pre-process BSData
normOpts <- setNormOptions(minSize=10)
plotPreprocessing(BSDataRaw,normInd,normOpts,plotArray=1)
BSData <- preprocessBeadSet(BSDataRaw,normInd,normOpts)
print(BSData)
print(fData(BSData)[1:10,])
print(fvarMetadata(BSData))

#Convert to AlleleSetIllumina-object
BSRed <- createAlleleSet(BSData,beadInfo,normOpts)
print(BSRed)
print(fData(BSRed)[1:10,])
print(fvarMetadata(BSRed))

#Read pre-processed data directly into AlleleSetIllumina object
dataFiles <- makeFilenames('testdata',normOpts,rPath)
beadFile <- paste(rPath,'beadData_testdata.txt',sep='/')
beadInfo2 <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE)
BSRed <- createAlleleSetFromFiles(dataFiles[1:4],beadInfo=beadInfo2)
print(varLabels(BSRed))

## End(Not run)

beadarrayMSV documentation built on May 29, 2017, 9:07 a.m.