\name{createExonWeightFile}
 \alias{createExonWeightFile}
 \title{Calculate exon weights}

 \description{Creates an exon weight file useful for segmentation, by 
 down-weighting unreliable exons.}

 \usage{createExonWeightFile(gatk.tumor.files, gatk.normal.files, 
     exon.weight.file)}
 \arguments{
   \item{gatk.tumor.files}{A small number (1-3) of GATK tumor coverage samples.}

   \item{gatk.normal.files}{A large number of GATK normal coverage samples (>20) 
 to estimate exon log-ratio standard deviations.}

   \item{exon.weight.file}{Output filename.}
 }
 
 \value{A data.frame with exon weights.}
 
 \author{Markus Riester}
 
 
 
 
 \examples{
 exon.weight.file <- "exon_weights.txt"
 gatk.normal.file <- system.file("extdata", "example_normal.txt", package="PureCN")
 gatk.normal2.file <- system.file("extdata", "example_normal2.txt", package="PureCN")
 gatk.normal.files <- c(gatk.normal.file, gatk.normal2.file)
 gatk.tumor.file <- system.file("extdata", "example_tumor.txt", package="PureCN")
 
 createExonWeightFile(gatk.tumor.file, gatk.normal.files, exon.weight.file)
 }