Package index • coMMpass

Data Acquisition

Download RNA-seq and clinical data from GDC and AWS S3

acquire_commpass_data(): Main data acquisition function
download_clinical_data(): Download clinical data from GDC
download_gdc_rnaseq(): Download RNA-seq data from GDC
download_s3_subset(): Download a Sample of RNA-seq Files from S3
get_commpass_clinical(): Query GDC for CoMMpass Clinical Data
list_s3_commpass(): List AWS S3 CoMMpass Bucket Contents
query_commpass_rna(): Query GDC for CoMMpass RNA-seq Metadata

Data Cleaning

Clean and integrate clinical and expression data

clean_clinical_data(): Clean Clinical Data
clean_expression_data(): Clean Expression Data
clean_treatment_data(): Clean and standardize treatment data
integrate_clinical_expression(): Create Integrated Dataset
summarize_treatment(): Summarize treatment lines per patient

Data Dictionary

Variable documentation and metadata

get_commpass_data_dictionary(): Get CoMMpass Data Dictionary
get_variable_docs(): Get Extended Documentation for a Variable

Quality Control

QC metrics, filtering, and normalization

calculate_qc_metrics(): Calculate QC metrics for RNA-seq data

Differential Expression

DESeq2, edgeR, limma-voom, consensus analysis, and DE visualization

compute_pca(): Compute PCA from transformed expression data
correlate_genes(): Correlate two genes across samples
correlate_genes_batch(): Batch correlation: one gene vs many
plot_gene_correlation(): Scatter plot of gene-gene correlation
plot_heatmap_de(): Heatmap of top DE genes
plot_ma(): MA plot of DE results
plot_pca(): PCA plot
plot_volcano(): Volcano plot of DE results
run_deseq2(): Run DESeq2 differential expression analysis
run_vst(): Run variance stabilizing transformation
summarize_de_methods(): Summarize DE results across methods

Survival Analysis

Kaplan-Meier, Cox PH, forest plots, marker-stratified survival

extract_risk_table(): Extract risk table from Kaplan-Meier results
plot_forest(): Plot forest plot of Cox hazard ratios
plot_km(): Plot Kaplan-Meier curve
prepare_survival_data(): Prepare survival data from clinical and cytogenetic data
run_cox_regression(): Run Cox proportional hazards regression
run_kaplan_meier(): Run Kaplan-Meier analysis
run_km_by_expression(): Run KM analysis stratified by gene expression level
run_km_by_markers(): Run KM analysis for each individual cytogenetic marker

Pathway Analysis

GSEA, ORA, MSigDB gene sets, gene annotation, enrichment visualization

annotate_de_results(): Add gene symbol column to DE results table
annotate_genes(): Annotate Ensembl gene IDs with symbols and descriptions
plot_enrichment_barplot(): Bar plot of enrichment results
plot_enrichment_dotplot(): Dot plot of enrichment results
plot_gsea_running_score(): GSEA running enrichment score plot
run_gsea(): Run Gene Set Enrichment Analysis (GSEA)
run_ora(): Run Over-Representation Analysis (ORA)
run_pathway_analysis(): Run pathway enrichment analysis

Cytogenetics

FISH/cytogenetic extraction, risk classification, oncoprint, co-occurrence

calculate_cooccurrence(): Calculate pairwise co-occurrence of cytogenetic alterations
compute_riss(): Compute Revised International Staging System (R-ISS)
extract_cytogenetic_data(): Extract cytogenetic markers from clinical data
plot_cooccurrence_heatmap(): Plot co-occurrence heatmap of cytogenetic alterations
plot_cytogenetic_oncoprint(): Plot cytogenetic oncoprint
plot_expression_by_subtype(): Plot gene expression by cytogenetic subtype
summarize_cytogenetics(): Summarize cytogenetic alteration frequencies

Causal Analysis

Causal DAGs, adjustment sets, and model adequacy checks

commpass_dag(): Define the CoMMpass causal DAG
get_adjustment_sets(): Get adjustment sets for a given analysis
plot_dag(): Plot the CoMMpass causal DAG
check_adjustment(): Compare model covariates against DAG-implied adjustments

Storage

DuckDB-backed parquet querying

get_commpass_tbl(): Get Lazy DuckDB Table for CoMMpass Data
query_commpass_parquet(): Query CoMMpass Parquet Files

API

Plumber API endpoints for programmatic data access

api_get_clinical(): Get clinical data for API response
api_get_de_results(): Get DE results for API response
api_get_pathways(): Get pathway analysis results for API response
api_get_survival(): Get survival data for API response
api_list_datasets(): List available API datasets
api_serve(): Launch the plumber API
generate_api_endpoint(): Generate a single API endpoint JSON string
generate_api_index(): Generate API index metadata

Utilities

Shared helpers for formatting and summaries

create_summary_table(): Create Summary Statistics Table
example_data(): Load example coMMpass datasets
export_h5ad(): Export SummarizedExperiment to H5AD (AnnData) format
format_file_size(): Format File Size in Human-Readable Format
format_with_commas(): Format Number with Thousands Separator
gene_report(): Render a single-gene characterization report
get_counts_assay(): Get counts assay from SummarizedExperiment
strip_plotly(): Strip plotly closure bloat for compact serialization

Internal

Internal helper functions (not exported)

check_dependencies(): Check package dependencies
create_project_dirs(): Create project directories
download_aws_data(): Download data from AWS S3 open access bucket
filter_low_quality(): Filter low-quality samples and genes
find_consensus_genes(): Find consensus DE genes across methods
generate_summary_report(): Generate summary report
normalize_rnaseq(): Normalize RNA-seq data
render_de_report(): Render DE analysis report
run_edger(): Run edgeR differential expression analysis
run_limma(): Run limma differential expression analysis
save_timestamped(): Save results with timestamp
setup_logging(): Setup logging
summarize_data(): Generate summary statistics