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Add published mutational signatures to pancan_pcawg_2020 (#1824)
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* add published mutational signatures pcawg

* rename matrix to counts

* filter DBS counts

* fix letter casing in profile name

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Co-authored-by: Ramya Madupuri <[email protected]>
Co-authored-by: rmadupuri <[email protected]>
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22 changes: 22 additions & 0 deletions public/pancan_pcawg_2020/README.md
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# Mutational Signatures inclusion
The original publication contains [mutational signature activity scores](https://www.synapse.org/#!Synapse:syn11804065)
extracted by SigProfiler.

## Input files
- [single-base substitution signature activity](https://www.synapse.org/#!Synapse:syn11738669) - PCAWG_sigProfiler_SBS_signatures_in_samples.csv
- [double-base substitution signature activity](https://www.synapse.org/#!Synapse:syn11738667) - PCAWG_sigProfiler_DBS_signatures_in_samples.csv
- [insertion-deletion signature activity](https://www.synapse.org/#!Synapse:syn11738668) - PCAWG_SigProfiler_ID_signatures_in_samples.csv
- [mutations](data_mutations.txt) - data_mutations.txt

## Contribution files
The original files contain activity scores. Activity and contribution scores can be calculated from each other.
For each signature type (SBS/DBS/INDEL) the contribution scores were calculated per sample as follows:
```
contribution (signature x) = activity (signature x) / total activity of all signatures in sample
```
Only samples present in the cBioPortal study were included.

## Mutational matrix
The mutational matrix was extracted from the `data_mutations.txt` file using SigProfilerMatrixGenerator python package
(v1.2.15) and the included reference genome GRCh37 (`SigProfilerMatrixGenerator.install.install('GRCh37')`).
Only samples with contribution scores were included.
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cancer_study_identifier: pancan_pcawg_2020
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: MUTATIONAL_SIGNATURE
datatype: LIMIT-VALUE
stable_id: mutational_signatures_contribution_DBS
profile_name: Mutational signatures contribution DBS
profile_description: Mutational signature contribution, calculated from PCAWG DBS activity
data_filename: data_mutational_signatures_contribution_DBS.txt
show_profile_in_analysis_tab: true
generic_entity_meta_properties: NAME,DESCRIPTION,URL
value_sort_order: DESC
pivot_threshold_value: 0.0
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cancer_study_identifier: pancan_pcawg_2020
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: MUTATIONAL_SIGNATURE
datatype: LIMIT-VALUE
stable_id: mutational_signatures_contribution_ID
profile_name: Mutational signatures contribution ID
profile_description: Mutational signature contribution, calculated from PCAWG ID activity
data_filename: data_mutational_signatures_contribution_ID.txt
show_profile_in_analysis_tab: true
generic_entity_meta_properties: NAME,DESCRIPTION,URL
value_sort_order: DESC
pivot_threshold_value: 0.0
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cancer_study_identifier: pancan_pcawg_2020
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: MUTATIONAL_SIGNATURE
datatype: LIMIT-VALUE
stable_id: mutational_signatures_contribution_SBS
profile_name: Mutational signatures contribution SBS
profile_description: Mutational signature contribution, calculated from PCAWG SBS activity
data_filename: data_mutational_signatures_contribution_SBS.txt
show_profile_in_analysis_tab: true
generic_entity_meta_properties: NAME,DESCRIPTION,URL
value_sort_order: DESC
pivot_threshold_value: 0.0
10 changes: 10 additions & 0 deletions public/pancan_pcawg_2020/meta_mutational_signatures_counts_DBS.txt
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cancer_study_identifier: pancan_pcawg_2020
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: MUTATIONAL_SIGNATURE
datatype: LIMIT-VALUE
stable_id: mutational_signatures_counts_DBS
profile_name: Mutational signatures counts DBS
profile_description: Mutational count matrix, extracted from data_mutations.txt using SigProfilerMatrixGenerator v1.2.15
data_filename: data_mutational_signatures_counts_DBS.txt
show_profile_in_analysis_tab: false
generic_entity_meta_properties: NAME
10 changes: 10 additions & 0 deletions public/pancan_pcawg_2020/meta_mutational_signatures_counts_ID.txt
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cancer_study_identifier: pancan_pcawg_2020
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: MUTATIONAL_SIGNATURE
datatype: LIMIT-VALUE
stable_id: mutational_signatures_counts_ID
profile_name: Mutational signatures counts ID
profile_description: Mutational count matrix, extracted from data_mutations.txt using SigProfilerMatrixGenerator v1.2.15
data_filename: data_mutational_signatures_counts_ID.txt
show_profile_in_analysis_tab: false
generic_entity_meta_properties: NAME
10 changes: 10 additions & 0 deletions public/pancan_pcawg_2020/meta_mutational_signatures_counts_SBS.txt
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cancer_study_identifier: pancan_pcawg_2020
genetic_alteration_type: GENERIC_ASSAY
generic_assay_type: MUTATIONAL_SIGNATURE
datatype: LIMIT-VALUE
stable_id: mutational_signatures_counts_SBS
profile_name: Mutational signatures counts SBS
profile_description: Mutational count matrix, extracted from data_mutations.txt using SigProfilerMatrixGenerator v1.2.15
data_filename: data_mutational_signatures_counts_SBS.txt
show_profile_in_analysis_tab: false
generic_entity_meta_properties: NAME

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