| Authors: | Komal S. Rathi
Adam Kraya Run Jin |
|---|---|
| Contact: | RATHIK@chop.edu, KRAYAA@chop.edu, JINR@chop.edu |
| Organization: | D3B, CHOP |
| Status: | This is "work in progress" |
| Date: | 2024-09-18 |
This repo is obsolete. Please refer to https://github.com/d3b-center/d3b-patient-report-analysis for up-to-date reporting code.
- Clone the OMPARE repository.
- Install R packages:
# install packages
cd /path-to/OMPARE
Rscript code/utils/install_pkgs.R
# NOTE: ggnetwork v0.5.1 is required- Download reference data:
# get reference data from s3
aws s3 --profile Mgmt-Console-Dev-chopd3bprod@684194535433 sync s3://d3b-bix-dev-data-bucket/PNOC008/data /path-to/OMPARE/data/
# chembldb v29 needs to be downloaded separately
# download chembldb v29 from https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_29_sqlite.tar.gz and save under data/chembl directory, then untar it. You will find the database under the path: data/chembl/chembl_29_sqlite/chembl_29.db.- Download patient-specific files from data delivery project:
- Copy Number:
{uuid}.controlfreec.info.txt(for purity and ploidy){uuid}.gainloss.txt{uuid}.diagram.pdf
- Expression:
{uuid}.genes.results
- Fusions:
{uuid}.arriba.fusions.tsv{uuid}.STAR.fusion_predictions.abridged.coding_effect.tsv
- Somatic Variants:
{uuid}.{lancet, mutect2, strelka2, vardict}_somatic.norm.annot.protected.maf{uuid}.consensus_somatic.protected.maf
- Germline Variants:
{uuid}.gatk.PASS.vcf.gz.hg38_multianno.txt.gz
- Download the following clinical information files and add data manually to
data/manifest/manifest.xlsx
- Files from Kids First DRC
- PNOC008 Clinical Manifest (needed to map
Research IDto ADAPTcohort_participant_id)
- PNOC008 Clinical Manifest (needed to map
- Currently, we have switched to using data assembly histology file available with each new patient: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/sd-8y99qzjj-data-assembly/
Note: None of these files have information on short_histology or broad_histology so currently it is being hard-coded HGAT and Diffuse astrocytic and oligodendroglial tumor, respectively.
run_OMPARE.R: Master script that runs the following scripts:
- code/create_project_dir.R: create project directory and organize files.
- code/create_clinfile.R: create clinical file for patient of interest.
- code/update_pnoc008_matrices.R: update PNOC008 data matrices (cnv, mutations, fusions, expression) with each new patient.
- OMPARE.Rmd: run html reports
- Sync back updated data folder to s3:
aws s3 --profile Mgmt-Console-Dev-chopd3bprod@684194535433 sync data s3://d3b-bix-dev-data-bucket/PNOC008/data/ --exclude 'chembl/*' - upload_reports.R: upload reports and output folders to PNOC008 data delivery project on cavatica.
Options:
--patient=PATIENT
Patient identifier (PNOC008-22, C3342894...)
--source_dir=SOURCE_DIR
Source directory with all files
--clin_file=CLIN_FILE
Manifest file (.xlsx)
--sync_data=SYNC_DATA
Sync reference data to s3 (TRUE or FALSE)
--upload_reports=UPLOAD_REPORTS
Upload reports to cavatica (TRUE or FALSE)
--study=STUDY
Study ID (PNOC008 or CBTN)
# Example for patient PNOC008-40
Rscript run_OMPARE.R \
--patient PNOC008-40 \
--sourcedir ~/Downloads/p40 \
--clin_file data/manifest/pnoc008_manifest.xlsx \
--sync_data TRUE \
--upload_reports FALSE \
--study PNOC008code/create_project_dir.R: this script creates and organizes input files under results. Creates output folder to store all output for plots and tables reported and reports folder to store all html output.
Rscript code/create_project_dir.R --help
Options:
--sourcedir=SOURCEDIR
Source directory with all files
--destdir=DESTDIR
Destination directory.
# Example for patient PNOC008-40
Rscript code/create_project.R \
--sourcedir ~/Downloads/p40 \
--destdir /path-to/OMPARE/results/PNOC008-40code/create_clinfile.R: this script creates clinical file for patient of interest and stores under results/PNOC008-XX/clinical/.
Rscript code/create_clinfile.R --help
Options:
--sheet=SHEET
PNOC008 Manifest file (.xlsx)
--dir=DIR
Path to PNOC008 patient folder.
--patient=PATIENT
Patient identifier for PNOC008. e.g. PNOC008-1, PNOC008-10 etc
# Example for patient PNOC008-40
Rscript code/create_clinfile.R \
--sheet /path-to/OMPARE/data/manifest/pnoc008_manifest.xlsx \
--patient PNOC008-40 \
--dir /path-to/OMPARE/results/PNOC008-40NOTE: The above steps will create a directory structure for the patient of interest:
# Example for PNOC008-40
.
results/PNOC008-40
├── clinical
│ └── patient_report.txt
├── copy-number-variations
│ ├── {uuid}.controlfreec.info.txt
│ ├── {uuid}.diagram.pdf
│ └── {uuid}.gainloss.txt
├── gene-expressions
│ └── {uuid}.rsem.genes.results.gz
├── gene-fusions
│ ├── {uuid}.STAR.fusion_predictions.abridged.coding_effect.tsv
│ └── {uuid}.arriba.fusions.tsv
├── output
├── reports
└── simple-variants
├── {uuid}.lancet_somatic.norm.annot.protected.maf
├── {uuid}.mutect2_somatic.norm.annot.protected.maf
├── {uuid}.strelka2_somatic.norm.annot.protected.maf
├── {uuid}.vardict_somatic.norm.annot.protected.maf
├── {uuid}.consensus_somatic.protected.maf
└── {uuid}.gatk.PASS.vcf.gz.hg38_multianno.txt.gzcode/update_pnoc008_matrices.R: this script updates the 008 patient matrices (cnv, mutations, fusions, expression) by adding current patient of interest
Rscript code/update_pnoc008_matrices.R
# Running the script will update the following files:
data/pnoc008
├── pnoc008_clinical.rds
├── pnoc008_cnv_filtered.rds
├── pnoc008_consensus_mutation_filtered.rds
├── pnoc008_counts_matrix.rds
├── pnoc008_fpkm_matrix.rds
├── pnoc008_fusions_filtered.rds
├── pnoc008_tmb_scores.rds
├── pnoc008_tpm_matrix.rds
└── pnoc008_vs_gtex_brain_degs.rdsGenerate markdown report:
# patient_dir is the project directory of current patient
# set_title is the title for the report. (Optional)
# snv_pattern is one of the six values for simple variants: lancet, mutect2, strelka2, vardict, consensus, all (all four callers together)
Rscript -e "rmarkdown::render(input = 'OMPARE.Rmd',
params = list(patient_dir = patient_dir,
set_title = set_title,
snv_caller = snv_caller),
output_dir = output_dir,
intermediates_dir = output_dir,
output_file = output_file, clean = TRUE)"After running the reports, the project folder will have all output files with plots and tables under output and all html reports under reports:
.
├── drug_recommendations
│ ├── CEMITools
│ │ ├── beta_r2.pdf
│ │ ├── clustered_samples.rds
│ │ ├── diagnostics.html
│ │ ├── enrichment_es.tsv
│ │ ├── enrichment_nes.tsv
│ │ ├── enrichment_padj.tsv
│ │ ├── expected_counts_corrected.rds
│ │ ├── gsea.pdf
│ │ ├── hist.pdf
│ │ ├── hubs.rds
│ │ ├── interaction.pdf
│ │ ├── interactions.tsv
│ │ ├── mean_k.pdf
│ │ ├── mean_var.pdf
│ │ ├── module.tsv
│ │ ├── modules_genes.gmt
│ │ ├── ora.pdf
│ │ ├── ora.tsv
│ │ ├── parameters.tsv
│ │ ├── profile.pdf
│ │ ├── qq.pdf
│ │ ├── report.html
│ │ ├── sample_tree.pdf
│ │ ├── selected_genes.txt
│ │ ├── summary.rds
│ │ ├── summary_eigengene.tsv
│ │ ├── summary_mean.tsv
│ │ ├── summary_median.tsv
│ │ ├── umap_output.rds
│ │ └── umap_top_20_neighbors_output.rds
│ ├── GTExBrain_dsea_go_mf_output.html
│ ├── GTExBrain_dsea_go_mf_output.pdf
│ ├── GTExBrain_dsea_go_mf_output.txt
│ ├── GTExBrain_dsea_go_mf_output_files
│ ├── GTExBrain_qSig_output.txt
│ ├── GTExBrain_tsea_reactome_output.txt
│ ├── PBTA_ALL_dsea_go_mf_output.html
│ ├── PBTA_ALL_dsea_go_mf_output.pdf
│ ├── PBTA_ALL_dsea_go_mf_output.txt
│ ├── PBTA_ALL_dsea_go_mf_output_files
│ ├── PBTA_ALL_qSig_output.txt
│ ├── PBTA_ALL_tsea_reactome_output.txt
│ ├── PBTA_HGG_dsea_go_mf_output.html
│ ├── PBTA_HGG_dsea_go_mf_output.pdf
│ ├── PBTA_HGG_dsea_go_mf_output.txt
│ ├── PBTA_HGG_dsea_go_mf_output_files
│ ├── PBTA_HGG_qSig_output.txt
│ ├── PBTA_HGG_tsea_reactome_output.txt
│ ├── {patient_id}_CHEMBL_drug-gene.tsv
│ ├── drug_dge_density_plots
│ │ ├── {gene}_drug_dge_density_plots.png
│ │ └── top_drug_dge_density_plots.pdf
│ ├── drug_pathways_barplot.pdf
│ ├── ora_plots.pdf
│ └── transcriptome_drug_rec.rds
├── drug_synergy
│ ├── combined_qSig_synergy_score.tsv
│ ├── combined_qSig_synergy_score_top10.pdf
│ ├── gtex_qSig_subnetwork_drug_gene_map.tsv
│ ├── gtex_qSig_synergy_score.tsv
│ ├── pbta_hgg_qSig_subnetwork_drug_gene_map.tsv
│ ├── pbta_hgg_qSig_synergy_score.tsv
│ ├── pbta_qSig_subnetwork_drug_gene_map.tsv
│ ├── pbta_qSig_synergy_score.tsv
│ ├── subnetwork_gene_drug_map.tsv
│ └── subnetwork_genes.tsv
├── filtered_germline_vars.rds
├── genomic_landscape_plots
│ └── circos_plot.png
├── immune_analysis
│ ├── immune_scores_adult.pdf
│ ├── immune_scores_adult.rds
│ ├── immune_scores_pediatric.pdf
│ ├── immune_scores_pediatric.rds
│ ├── immune_scores_topcor_pediatric.pdf
│ ├── immune_scores_topcor_pediatric.rds
│ ├── tis_scores.pdf
│ └── tis_scores.rds
├── oncogrid_analysis
│ └── complexheatmap_oncogrid.pdf
├── oncokb_analysis
│ ├── oncokb_cnv.txt
│ ├── oncokb_cnv_annotated.txt
│ ├── oncokb_fusion.txt
│ ├── oncokb_fusion_annotated.txt
│ ├── oncokb_{snv_caller}_annotated.txt
│ ├── oncokb_merged_{snv_caller}_annotated.txt
│ └── oncokb_merged_{snv_caller}_annotated_actgenes.txt
├── rnaseq_analysis
│ ├── {patient_id}_summary_DE_Genes_Down.txt
│ ├── {patient_id}_summary_DE_Genes_Up.txt
│ ├── {patient_id}_summary_Pathways_Down.txt
│ ├── {patient_id}_summary_Pathways_Up.txt
│ ├── diffexpr_genes_barplot_output.rds
│ ├── diffreg_pathways_barplot_output.rds
│ └── rnaseq_analysis_output.rds
├── survival_analysis
│ ├── kaplan_meier_adult.pdf
│ └── kaplan_meier_pediatric.pdf
├── tmb_analysis
│ ├── consensus_mpf_output.txt
│ ├── tmb_profile_output.rds
│ └── tumor_signature_output.rds
└── transcriptomically_similar_analysis
├── dim_reduction_plot_adult.rds
├── dim_reduction_plot_pediatric.rds
├── lollipop_recurrent_adult.pdf
├── lollipop_recurrent_pediatric.pdf
├── lollipop_shared_adult.pdf
├── lollipop_shared_pediatric.pdf
├── mutational_analysis_adult.rds
├── mutational_analysis_pediatric.rds
├── mutational_cnv_recurrent_adult.pdf
├── mutational_cnv_recurrent_pediatric.pdf
├── mutational_cnv_shared_adult.pdf
├── mutational_cnv_shared_pediatric.pdf
├── mutational_recurrent_adult.pdf
├── mutational_recurrent_pediatric.pdf
├── mutational_shared_adult.pdf
├── mutational_shared_pediatric.pdf
├── pathway_analysis_adult.pdf
├── pathway_analysis_adult.rds
├── pathway_analysis_pediatric.pdf
├── pathway_analysis_pediatric.rds
├── pbta_hgat_pnoc008_nn_table.rds
├── pbta_hgat_pnoc008_umap_output.rds
├── pbta_pnoc008_nn_table.rds
├── pbta_pnoc008_umap_output.rds
├── ssgsea_scores_pediatric.pdf
├── ssgsea_scores_pediatric.rds
├── tcga_gbm_pnoc008_nn_table.rds
├── tcga_pnoc008_umap_output.rds
├── transciptomically_similar_adult.rds
└── transciptomically_similar_pediatric.rdsupload_reports.R: this script uploads the files under reports and output folders to the data delivery project folder on cavatica.
Rscript upload_reports.R --help
Options:
--patient=PATIENT
Patient Identifier (PNOC008-22, etc...)
--study=STUDY
PNOC008 or CBTN
# Example run for PNOC008-40
Rscript upload_reports.R \
--patient PNOC008-40 \
--study 'PNOC008'These hgg-dmg files are 20201202-data version dependent:
hgg-dmg-integration
└── 20201202-data
├── CC_based_heatmap_Distance_euclidean_finalLinkage_average_clusterAlg_KM_expct_counts_VST_cluster_and_annotation.tsv
├── pbta-hgat-dx-prog-pm-gene-counts-rsem-expected_count-uncorrected.rds
└── pbta-histologies.tsv