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#' # Calculation of mutation copy numbers and timing parameters
#' Minimal example
#' source("/Users/mg14/Projects/PCAWG-11/code/MutationTime.R")
#' vcf <- readVcf("final/final_consensus_12oct_passonly/snv_mnv/0040b1b6-b07a-4b6e-90ef-133523eaf412.consensus.20160830.somatic.snv_mnv.vcf.gz",genome="GRCh37")
#' bb <- loadBB("dp/20161213_vanloo_wedge_consSNV_prelimConsCNAallStar/4_copynumber/0040b1b6-b07a-4b6e-90ef-133523eaf412_segments.txt.gz")
#' clusters = read.table("dp/20161213_vanloo_wedge_consSNV_prelimConsCNAallStar/2_subclones/0040b1b6-b07a-4b6e-90ef-133523eaf412_subclonal_structure.txt.gz", header=TRUE, sep="\t")
#' purityPloidy <- read.table("dp/20161213_vanloo_wedge_consSNV_prelimConsCNAallStar/1_purity_ploidy/purity_ploidy.txt, header=TRUE, sep="\t")
#' purity <- purityPloidy[2,2]
#' MCN <- computeMutCn(vcf[1:1000], bb, clusters, purity)
#' # Check output

mg14

#' Supplementary Data 2
#' =======================
#' ### Supplementary code and figures accompanying *Interconnections among mutations, gene expression, clinical variables and patient outcome in myelodysplastic syndromes*
#' 
#' This document contains the complete code used in the analysis. It is purely written in `R` using a series of `R` and `Bioconductor` packages. 
#' This report has been generated using the `knitr` R package (http://yihui.name/knitr/). 
#' For a complete list of packages and their versions please have a look at the end of this document.

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