This repository contains code and metadata for the glioblastoma progression study (https://www.nature.com/articles/s41591-018-0156-x or https://www.biorxiv.org/content/early/2017/08/09/173864). The data analysis code in src relies on the processed data (methylation calls, PDR calls, statistics) being available in the directory structure produced by a data processing pipeline based on Pypiper (https://pypiper.readthedocs.io) and Looper (https://looper.readthedocs.io) as specified in the project configuration file. It further relies on the projectInit R package to read the pipeline results into R for further analysis. Specifically an early version of this package was used: project.init. The scripts found in this repository are meant to be executed in order and produce the plots and tables presented in the corresponding publication.
Addititional data can be found on the supplementary website: http://glioblastoma-progression.computational-epigenetics.org
Additionally to the links between figures and scripts listed below, the positions in the scripts where the respective plots are produced are marked with ####Figure X.
The combined annotation tables used in nearly every analysis are produced using the scripts 01.1-combine_annotation.R (combining the different types of collected annotations) and 10.1_add_annotation.R (adding annotations produced through analysis e.g. transcriptional subtypes) and stored in the folder 01.1-combined_annotation.
| Figure | Scripts | Results |
|---|---|---|
| 1a | Overview schematic --> No script | No analysis |
| 1b | 01.2-sample_stats.R | 01.2-sample_stats |
| 1c | 02.4-meth_overview_tracks.R | 02-meth_overview |
| 1d | 02.2-IDH1_TurcanEtAl.R | 02-meth_overview |
| 2a | Overview schematic --> No script | No analysis |
| 2b | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| 2c | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| 2d | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| 2e | 08.1-GBM_classifier.R + 13.1-survival_analysis.R | 13.1-survival |
| 2f | 08.1-GBM_classifier.R + 11.3-DiffMeth_groups.R + 11.4-LOLA.R | 11.3-DiffMeth_groups |
| 2g | 08.1-GBM_classifier.R + 11.3-DiffMeth_groups.R + 11.4-LOLA.R | 11.3-DiffMeth_groups |
| 2h | Overview schematic --> No script | No analysis |
| 2i | 08.1-GBM_classifier.R + 09.1-dipScore.R + 12.1-Annotation_Association_folow-up.R | 09-dipScore + 12.1-Annot_Associations_follow-up |
| 3a | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| 3b | Histology --> No script | No analysis |
| 3c | 13.1-survival_analysis.R | 13.1-survival |
| 3d | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| 3e | Histology --> No script | No analysis |
| 3e | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| 3g | 08.2-meth_pred.R | 08.2-meth_pred |
| 4a | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| 4b | 13.1-survival_analysis.R | 13.1-survival |
| 4c | 08.2-meth_pred.R | 08.2-meth_pred |
| 4d | 08.2-meth_pred.R | 08.2-meth_pred |
| 4e | 08.2-meth_pred.R | 08.2-meth_pred |
| 4f | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| 4g | Histology --> No script | No analysis |
| 4h | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| 4i | 08.2-meth_pred.R | 08.2-meth_pred |
| 4j | 13.1-survival_analysis.R | 13.1-survival |
| 5a | Overview schematic --> No script | No analysis |
| 5b | 05.1-pdr_caches.R + 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 07.1-meth_heterogeneity.R | 07-meth_heterogeneity |
| 5c | 05.1-pdr_caches.R + 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 07.1-meth_heterogeneity.R | 07-meth_heterogeneity |
| 5d | 05.1-pdr_caches.R + 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 07.1-meth_heterogeneity.R+13.1-survival_analysis.R | 13.1-survival |
| 5e | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R | 11.2-diffMeth_single |
| 6a | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R | 11.2-diffMeth_single |
| 6b | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R | 11.2-diffMeth_single |
| 6c | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R | 11.2-diffMeth_single |
| 6d | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R + 13.1-survival_analysis.R | 13.1-survival |
| 6e | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R | 11.2-diffMeth_single |
| 6f | 11.1-diffMeth.R + 11.2-prom_diffMeth_single.R + 13.1-survival_analysis.R | 13.1-survival |
| 6g | 08.2-meth_pred.R | 08.2-meth_pred |
| 6h | 08.2-meth_pred.R | 08.2-meth_pred |
| S1a | 01.2-sample_stats.R | 01.2-sample_stats |
| S1b | 01.2-sample_stats.R | 01.2-sample_stats |
| S1c | 01.2-sample_stats.R | 01.2-sample_stats |
| S1d | 01.2-sample_stats.R | 01.2-sample_stats |
| S1e | 02.4-meth_overview_regions.R | 02-meth_overview |
| S1f | 02.4-meth_overview_regions.R | 02-meth_overview |
| S1g | 02.4-meth_overview_regions.R | 02-meth_overview |
| S1h | 02.4-meth_overview_regions.R | 02-meth_overview |
| S2a | 02.4-meth_overview_tracks.R | 02-meth_overview |
| S2b | 02.4-meth_overview_tracks.R | 02-meth_overview |
| S2c | 02.3-MGMT_meth.R | 02-meth_overview |
| S2d | 02.3-MGMT_meth.R + 13.1-survival_analysis.R | 13.1-survival |
| S3a | 03.2-run_CopywrtiteR.R + 03.3-plot_CopywrtiteR.R | 03-CopywriteR |
| S3b | 03.2-run_CopywrtiteR.R + 03.3-plot_CopywrtiteR.R + 13.1-survival_analysis.R | 13.1-survival |
| S3c | 03.2-run_CopywrtiteR.R + 03.3-plot_CopywrtiteR.R | 03-CopywriteR |
| S4a | 03.2-run_CopywrtiteR.R + 03.3-plot_CopywrtiteR.R + 03.4-validate_CopywrtiteR.R | 03-CopywriteR |
| S4b | 03.2-run_CopywrtiteR.R + 03.3-plot_CopywrtiteR.R + 03.4-validate_CopywrtiteR.R | 03-CopywriteR |
| S5a | Overview schematic --> No script | No analysis |
| S5b | 08.1-GBM_classifier.R + 08.1-GBM_classifier_validation.R | 08.1-GBM_classifier |
| S5c | 08.1-GBM_classifier.R + 08.1-GBM_classifier_validation.R | 08.1-GBM_classifier |
| S5d | 08.1-GBM_classifier.R + 08.1-GBM_classifier_validation.R | 08.1-GBM_classifier |
| S6a | Overview schematic --> No script | No analysis |
| S6b | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| S6c | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| S6d | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| S6e | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| S6f | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| S6g | 08.1-GBM_classifier.R | 08.1-GBM_classifier |
| S6h | 08.1-GBM_classifier.R + 13.1-survival_analysis.R | 13.1-survival |
| S7a | 08.1-GBM_classifier.R + 09.1-dipScore.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S7b | 08.1-GBM_classifier.R + 09.1-dipScore.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S7c | 08.1-GBM_classifier.R + 09.1-dipScore.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S7d | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S7e | 08.1-GBM_classifier.R + 09.1-dipScore.R + 12.1-Annotation_Association_folow-up.R | 09-dipScore |
| S7f | 08.1-GBM_classifier.R + 09.1-dipScore.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S8a | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S8b | Histology --> No script | No analysis |
| S8c | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S8d | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S8e | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S8f | 13.1-survival_analysis.R | 13.1-survival |
| S8g | 08.2-meth_pred.R | 08.2-meth_pred |
| S9a | MR images --> No script | No analysis |
| S9b | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S9c | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S9d | 08.1-GBM_classifier.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S9e | 13.1-survival_analysis.R | 13.1-survival |
| S9f | MR images --> No script | No analysis |
| S9g | 13.1-survival_analysis.R | 13.1-survival |
| S10a | Overview schematic --> No script | No analysis |
| S10b | 08.2-meth_pred.R | 08.2-meth_pred |
| S10c | 08.2-meth_pred.R | 08.2-meth_pred |
| S10d | 08.2-meth_pred.R | 08.2-meth_pred |
| S10e | 08.2-meth_pred.R | 08.2-meth_pred |
| S10f | 08.2-meth_pred.R | 08.2-meth_pred |
| S10g | 08.2-meth_pred.R | 08.2-meth_pred |
| S11a | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S11b | 13.1-survival_analysis.R | 13.1-survival |
| S11c | 08.2-meth_pred.R | 08.2-meth_pred |
| S11d | 08.2-meth_pred.R | 08.2-meth_pred |
| S11e | 08.2-meth_pred.R | 08.2-meth_pred |
| S11f | 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S12a | 05.1-pdr_caches.R + 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 07.1-meth_heterogeneity.R | 07-meth_heterogeneity |
| S12b | 05.1-pdr_caches.R + 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 07.1-meth_heterogeneity.R + 12.1-Annotation_Association_folow-up.R | 12.1-Annot_Associations_follow-up |
| S12c | 05.1-pdr_caches.R + 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 07.1-meth_heterogeneity.R + 13.1-survival_analysis.R | 13.1-survival |
| S12d | 06.1-submit_methclone.R + 06.2-analyse_methclone.R | 06-methclone |
| S12e | 06.1-submit_methclone.R + 06.2-analyse_methclone.R + 13.1-survival_analysis.R | 13.1-survival |
| S12f | 06.1-submit_methclone.R + 06.2-analyse_methclone.R | 06-methclone |
| S12g | 06.1-submit_methclone.R + 06.2-analyse_methclone.R | 06-methclone |
| S12h | 06.1-submit_methclone.R + 06.2-analyse_methclone.R | 06-methclone |
| 13 | Screenshots from the data explorer (http://glioblastoma-progression.computational-epigenetics.org) --> No script | No analysis |