parseSourceFile {VanillaICE} | R Documentation |
This function parses genome studio files, writing the low-level data for log R ratios, B allele frequencies, and genotypes to disk as integers (1 file per subject per data type).
parseSourceFile(object, param) ## S4 method for signature 'ArrayViews,CopyNumScanParams' parseSourceFile(object, param)
object |
An |
param |
An object of class |
ArrayViews
ArrayViews
CopyNumScanParams
require(BSgenome.Hsapiens.UCSC.hg18) bsgenome <- BSgenome.Hsapiens.UCSC.hg18 require(data.table) extdir <- system.file("extdata", package="VanillaICE", mustWork=TRUE) features <- suppressWarnings(fread(file.path(extdir, "SNP_info.csv"))) fgr <- GRanges(paste0("chr", features$Chr), IRanges(features$Position, width=1), isSnp=features[["Intensity Only"]]==0) fgr <- SnpGRanges(fgr) names(fgr) <- features[["Name"]] seqlevels(fgr) <- seqlevels(bsgenome)[seqlevels(bsgenome) %in% seqlevels(fgr)] seqinfo(fgr) <- seqinfo(bsgenome)[seqlevels(fgr),] fgr <- sort(fgr) files <- list.files(extdir, full.names=TRUE, recursive=TRUE, pattern="FinalReport") views <- ArrayViews(rowRanges=fgr, sourcePaths=files, parsedPath=tempdir()) show(views) ## read the first file dat <- fread(files[1], skip="[Data]") ## information to store on the markers select <- match(c("SNP Name", "Allele1 - AB", "Allele2 - AB", "Log R Ratio", "B Allele Freq"), names(dat)) ## ## which rows to keep in the MAP file. By matching on the sorted GRanges object ## containing the feature annotation, the low-level data for the log R ratios/ ## B allele frequencies will also be sorted ## index_genome <- match(names(fgr), dat[["SNP Name"]]) scan_params <- CopyNumScanParams(index_genome=index_genome, select=select) ## ## parse the source files ## parseSourceFile(views, scan_params) list.files(parsedPath(views)) ## ## Inspecting source data through accessors defined on the views object ## require(oligoClasses) ## log R ratios r <- head(lrr(views)) ## B allele frequencies b <- head(baf(views)) g <- head(genotypes(views))