Not counting markers classified as “FAIL” or “MONO-filt”, calculate the ratio of markers that are called for each array
In order to include pedigree errors,
BSRed must have an
"AlleleSetIllumina" object with an added
phenoData column “passRatio”. This is a numeric vector
holding the ratio of non-missing calls for each array
This function may be used to discard arrays with a low number of called markers. Note however that an array may be valuable even if the sample falls just outside the cluster borders for many markers (e.g. for a high intensity array). Should therefore be used with caution
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
## Not run: #Read pre-processed data directly into AlleleSetIllumina object rPath <- system.file("extdata", package="beadarrayMSV") normOpts <- setNormOptions() dataFiles <- makeFilenames('testdata',normOpts,rPath) beadFile <- paste(rPath,'beadData_testdata.txt',sep='/') beadInfo <- read.table(beadFile,sep='\t',header=TRUE,as.is=TRUE) BSRed <- createAlleleSetFromFiles(dataFiles[1:4],beadInfo=beadInfo) #Genotype calling BSRed <- callGenotypes(BSRed) BSRed <- validateCallsPedigree(BSRed) BSRed <- countFailedSNP(BSRed,inclPedErrors=TRUE) print(range(pData(BSRed)$passRatio)) #Plot highlighting markers to be discarded #NB! Such a high passRatio is not recommended indGoodArrays <- pData(BSRed)$passRatio > 0.6 plotGenotypes(BSRed,indHighlight=which(!indGoodArrays)) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.