AmplificationTimeR_paper_archive

A repository to store any code that was run as part of the AmplificationTimeR publication.

G Maria Jakobsdottir, Stefan C Dentro, Robert G Bristow, David C Wedge, AmplificationTimeR: An R Package for Timing Sequential Amplification Events, Bioinformatics, 2024;, btae281, https://doi.org/10.1093/bioinformatics/btae281

Overview of files and folders

• Generating_figures: A folder containing Rmarkdown documents for generating figures that form part of the AmplificationTimeR manuscript, as well as their html output, and session info files listing tools and programme versions.

  File	Description
  AmplificationTimeR_paper_figures_tables_analysis_080224.Rmd	Rmarkdown file with analysis and figures generated using PCAWG timing data.
  AmplificationTimeR_paper_figures_tables_analysis_080224.html	html file generated from the above Rmarkdown document.
  AmplificationTimeR_plotting_PCAWG_data_sessionInfo_2024-02-09.txt	session info for the above Rmarkdown and associated html file.
  plotting_cov_c8_wgd_csf3.Rmd	Rmarkdown document for analysis and plotting of 8q segments timed.
  plotting_cov_c8_wgd_csf3.html	html file generated from the above Rmarkdown document.
  plotting_cov_c8_sessionInfo_2024-02-08.txt	session info for the above Rmarkdown and associated html file.
  plotting_output_of_simulations_05_08.01.24_csf3.Rmd	Rmarkdown document for plotting figures from simulated data.
  plotting_output_of_simulations_05_08.01.24_csf3.nb.html	html file associated with the above Rmarkdown document.
  multinomial_plotting_simulation_sessionInfo_2024-01-08.txt	session info for the above Rmarkdown and html file.

• running_AmplificationTimeR: A folder containing code associated with running AmplificationTimeR on a portion of the PCAWG data set.

  File	Description
  20231123_running_AmplificationTimeR_on_PCAWG.R	R script used to run AmplificationTimeR on PCAWG data.
  AmplificationTimeR_run_sessionInfo_2024-01-06.txt	session info from most recent run of AmplificationTimeR on PCAWG data.

• running_cancerTiming: A folder containing code associated with running cancerTiming on a portion of the PCAWG data set.

  File	Description
  20230109_cancerTiming_PCAWG_MYC_BRCA_OV_PRAD.R	R script used to run cancerTiming on PCAWG data.
  sessionInfo_2023-01-09.txt	session info from the most recent run of cancerTiming on PCAWG data.

• running_MutationTimeR: A folder containing code associated with running MutationTimeR on a portion of the PCAWG data set.

  File	Description
  20230110_MutationTimeR_PCAWG_BRCA_OV_PRAD_all_array.R	R script used to run MutationTimeR on PCAWG data.
  collating_MutationTimeR_results_250123.R	R script to collate MutationTimeR timing data for segments spanning MYC.
  sessionInfo_2023-01-19.txt	session info from the most recent run of MutationTimeR on PCAWG data.

• Sample_mismatches:

  File	Description
  checking_sample_mismatches_070224.R	R script used to for identify and check inconsistencies in data between Battenberg and DPClust files in PCAWG data.

• SBS_classification_of_mutations:

  File	Description
  20221118_get_individual_mut_sigs_PCAWG.R	R script for working out mutational signature of individual mutations.

• Testing_with_simulated_data: A folder containing code associated with simulating data to test AmplificationTimeR

  File	Description
  testing_AmplificationTimeR_synthetic_multinomial_sampled_data_csf3.Rmd	Rmarkdown document for simulating timing data and testing the effect of varying mutation number and clocklike proportion.
  testing_AmplificationTimeR_synthetic_multinomial_sampled_data_csf3.html	html file generated from the above markdown document.
  multinomial_sampled_data_sessionInfo2024-01-08.txt	session info for the Rmarkdown document and html file above.
  testing_AmplificationTimeR_synthetic_mismatched_equations.Rmd	Rmarkdown document for simulating timing data and testing effect of applying mismatched equations.
  testing_AmplificationTimeR_synthetic_mismatched_equations.nb.html	html file generated from the above Rmarkdown document.
  multinomial_data_right_and_wrong_equations_sessionInfo_2024-01-05.txt	session info file for the above Rmarkdown and html document.

• Timing_8q_segments: A folder containing code for identifying and timing 8q segments for a portion of the PCAWG data set.

  File	Description
  20231116_list_all_8q_segments_BRCA_OV_PRAD.R	An Rscript to list all segments on 8q in the PCAWG BRCA, OV, and PRAD data.
  20231123_time_all_segments_on_8q_sbs1_sbs5_BRCA_OV_PRAD.R	R script to time all 8q segments in the aforementioned PCAWG data.
  BRCA_OV_PRAD_AmplificationTimeR_C8_results_sbs1_sbs5_sessionInfo2024-01-05.txt	session info associated with timing of the aforementioned 8q segments.