Description Usage Arguments Details Value Author(s) See Also Examples
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
1 2 3 4 5 6 7 8 9 | 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)
|
BSData |
|
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
|
normOpts |
List containing at least the elements “dist” and
“pNorm” (see |
includeAB |
If |
dataFiles |
Character vector containing filenames where the different
data-tables are saved (see |
markers |
Index to markers in the |
arrays |
Index to arrays/samples in the |
phenoInfo |
Data-table with phenotype data. Argument is ignored if “phFile” is provided in
|
sep |
Field delimiter in text-files (see |
quote |
Quote-marks used for character strings (see |
BSRed |
|
BSAdd |
|
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
Object of class "AlleleSetIllumina"
or "MultiSet"
Lars Gidskehaug
AlleleSetIllumina
,
MultiSet
, writeAlleleSet
,
makeFilenames
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ## 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)
|
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