This repository contains code used to analyze data reported in the Alberge, Dutta, Poletti, et al. paper.
Most data from the PCROWD study reported as average are available to other researchers upon request to Dr Ghobrial (mailto: Irene_Ghobrial [at] DFCI[dot]HARVARD[dot]EDU). Sequencing data will be made available shortly on the dbGAP study phsxxxx [New Stury Registered].
- Figure 1A
The code for figure and Fisher's Exact tests are in: code/2.1bis-create-new-matrix.R. Metadata are provided in Supplementary Table S1 (List of samples), S2 (List of MutSig2CV drivers), S3 (List of GISTIC2.0 drivers), S4 (Odds ratios and significance of driver enrichments), S9 (List of SV driver candidates from SSVGAR)
- Figure 1BCD
The code for figures and statistical tests is in code/2.2_compute-MM-like-score.R.
- Figure 2
Data is provided in Supplementary Table S5, exact lists of somatic mutations are accessible upon request with dbGAP access rights.
- Figure 3ABC
Timing data is provided in Supplementary Table S6, while code to perform the analysis are in code/5.1_clocklike-timing-EM-code.R and to reproduce the figures and statistical tests in code/5.2_clocklike-timing-figures-statistics.R.
- Figure 3D
Collaboration Dr. Kübler and Dr. Arndt [data to be uploaded].
- Figure 3E
Collaboration Dr. Poletti, Dr. Zamagni, Dr. Terragna, code and figures for the League Models are in TiMMing repository.
Code for Figure 3E is in code/5.3_clonality-league-comparison-bradley-terry-models-figure.R. Values from the model are provided in Supplementary Table S7.
- Figure 4A
Collaboration Dr. Coorens, code is in code/HDP_complete_workflow_TIMCOORENS.R and code/deconvolute_hdp_sigs_TIMCOORENS.R. Frequencies of substitutions are provided in Supplementary Table S8.
- Figure 4BC
Code is in code/3.2_signatures-corr-models-dup-ccf.R.
- Figure 5AB
Collaboration SSVGAR Loinaz, code is in companion repository SSVGAR), list of drivers is provided in Supplementary Table S9
- Figure 5C
Code is in code/2.5-SV-circos-MYC.R
- Figure 6A
Code is in code/6.1_DIG-noncoding-driver-analysis.R, detailed list of drivers is provided in Supplementary Table S10.
- Figure 6BC
Code is in code/6.2_noncoding-ILF2-promoter-zoom.R.
- Figure 6DE
Code is in code/6.3_noncoding-ILF2_commpass_expr.R, detailed participant IDs from the CoMMpass study and their mutational status is provided in Supplementary Table S11 and S12.