Moritz Gerstung mg14
mg14
/ ncomms6901-s3.R
Last active
May 19, 2018 06:08
Supplementary code and figures accompanying Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes doi:10.1038/ncomms6901
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| #' 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. | |
| #+ options, echo=FALSE, eval=TRUE | |
| options(width=120) |
mg14
/ MutationTime.R
Last active
May 22, 2020 09:21
[This has been migrated to https://github.com/gerstung-lab/MutationTime.R] Calculation of mutation copy numbers and timing parameters
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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 |