Add published mutational signatures to pancan_pcawg_2020 (#1824)

* add published mutational signatures pcawg

* rename matrix to counts

* filter DBS counts

* fix letter casing in profile name

---------

Co-authored-by: Ramya Madupuri <[email protected]>
Co-authored-by: rmadupuri <[email protected]>

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.

public/pancan_pcawg_2020/meta_mutational_signatures_contribution_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_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

public/pancan_pcawg_2020/meta_mutational_signatures_contribution_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_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

public/pancan_pcawg_2020/meta_mutational_signatures_contribution_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_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

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

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

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