VanillaICE (version 1.34.0)

parseSourceFile: Function for parsing GenomeStudio files

Description

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).

Usage

parseSourceFile(object, param)
"parseSourceFile"(object, param)

Arguments

object

An ArrayViews object

param

An object of class CopyNumScanParams

See Also

ArrayViews ArrayViews CopyNumScanParams

Examples

  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])
## 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))