# Personal Cancer Genome Reporter The Personal Cancer Genome Reporter (PCGR) is a stand-alone software workflow for functional annotation and translation of individual tumor genomes for precision cancer medicine. It interprets somatic SNVs/InDels and copy number aberrations, RNA fusions, and bulk RNA-seq expression data. The software classifies variants with respect to predicted *oncogenicity*, and clinical *actionability*. Interactive HTML output reports allow the user to interrogate the clinical impact of the molecular findings in an individual tumor. - Multi-omic data interpretation - Variant classification - according to *oncogenicity*: evaluating the oncogenic potential of somatic DNA aberrations ([ClinGen/CGC/VICC guidelines](https://pubmed.ncbi.nlm.nih.gov/35101336/)) - according to *actionability*: mapping the therapeutic, diagnostic, and prognostic implications of somatic DNA aberrations ([AMP/ASCO/CAP guidelines](https://pubmed.ncbi.nlm.nih.gov/27993330/)) - Tumor mutational burden (TMB) estimation - Mutational signature analysis - Microsatellite instability (MSI) classification - RNA-seq support - gene expression outlier detection, sample similarity analysis, and immune contexture profiling PCGR supports both of the most recent human genome assemblies (GRCh37/GRCh38), and accepts variant calls from both tumor-control and tumor-only sequencing assays. Much of the functionality is intended for whole-exome/whole-genome sequencing assays, but you can also apply PCGR to output from targeted sequencing panels. If you are interested in the interrogation of germline variants and their relation to cancer predisposition, we recommend trying the accompanying tool [Cancer Predisposition Sequencing Reporter (CPSR)](https://github.com/sigven/cpsr). Seven snapshots of sections in the [quarto](https://quarto.org)-based cancer genome report by PCGR (artificial sample, with more findings than usual): ![Variant classification - oncogenicity](img/pcgr_oncogenicity.png) ![Clinical actionability classification](img/pcgr_actionability.png) ![Somatic CNAs](img/pcgr_cna.png) ![Tumor mutational burden](img/pcgr_tmb.png) ![Gene expression outliers](img/pcgr_expression_outliers.png) ![Variant statistics](img/pcgr_variant_stats.png) ![Somatic RNA fusions](img/pcgr_rna_fusions.png) PCGR originates from the [Institute for Cancer Research, Oslo University Hospital, Norway](https://radium.no). ### Top News - *August 10th 2026*: **2.3.2 release** - patch to fix [issue \#300](https://github.com/sigven/pcgr/issues/300) and [issue \#302](https://github.com/sigven/pcgr/issues/302) - *July 10th 2026*: **2.3.1 release** - patch to fix [issue \#297](https://github.com/sigven/pcgr/issues/297) - *June 23rd 2026*: **2.3.0 release** - Data/software updates: - Ensembl VEP `v115` / GENCODE v49 - ClinVar (2026-06) - CIViC (2026-06-20) - and more - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *September 17th 2025:* **2.2.5 release** - fixed failing support for AD/AF filtering, adding AD filtering - skip processing when no PASS variants detected in input VCF - more streamlined plotting functions in quarto report templates - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *September 8th 2025:* **2.2.4 release** - various minor bug fixes, addition of `--sex` option for sex-adjusted CNA annotation - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 18th 2025:* **2.2.3 release** - Ensembl VEP `v113.4` - *July 15th 2025:* **2.2.2 release** - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *March 23rd 2025:* **2.2.1 release** - fix bug in CPSR for ClinVar variants with non-standard significance levels - *March 22nd 2025:* **2.2.0 release** - Data/software updates: - Ensembl VEP `v113` / GENCODE v47 - ClinVar (2025-03) - CIViC (2025-03-13) - and more - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *October 21st 2024:* **2.1.2 release** - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *October 11th 2024:* **2.1.1 release** - patch to fix [bug](https://github.com/sigven/pcgr/issues/252) with parsing of relative CDS start positions - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *September 29th 2024*: **2.1.0 release** - updated bundle, more oncogenic variants, CNA visualization, improved RNA-seq support, bug fixes, and more - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *August 1st 2024*: **2.0.3 release** - patch to fix purity/ploidy propagation, MAF output for tumor-only runs, and other minor issues - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 16th 2024*: **2.0.2 release** - patch to ensure correct reference to actionability guidelines - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *July 7th 2024*: **2.0.1 release** - patch with bug fix for mitochondrial input variants ([pr245](https://github.com/sigven/pcgr/pull/245)) - [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - *June 2024*: **2.0.0 release** - Details in [CHANGELOG](https://sigven.github.io/pcgr/articles/CHANGELOG.html) - Massive reference data bundle upgrade, new report layout, oncogenicity classification++ - Support for Singularity/Apptainer - Major data/software updates: - Ensembl VEP `v112` - ClinVar (2024-06) - CIViC (2024-06-21) - GENCODE `v46/v19` (GRCh38/GRCh37) - CancerMine `v50` (2023-03) - UniProt KB `v2024_03` ## Example reports [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20795653.svg)](https://doi.org/10.5281/zenodo.20795653) ## Why use PCGR? The great complexity of acquired mutations in individual tumor genomes poses a severe challenge for clinical interpretation. PCGR aims to be a comprehensive reporting platform that can - systematically interrogate tumor-specific variants in the context of known therapeutic, diagnostic, and prognostic biomarkers - highlight genomic aberrations with likely oncogenic potential - evaluate complex biomarker readouts (MSI, TMB, mutational signatures, gene expression outliers) - provide a structured and concise summary of the most relevant findings - present the results in a format accessible to clinical experts PCGR integrates a [comprehensive set of knowledge resources](https://sigven.github.io/pcgr/articles/annotation_resources.md) related to tumor biology and therapeutic biomarkers, both at the gene, and at the level of individual variants. The software generates a comprehensive molecular interpretation report that supports the translation of individual cancer genomes towards molecularly guided treatment strategies. ## Getting started - [Installation instructions](https://sigven.github.io/pcgr/articles/installation.md) - [Run through an example](https://sigven.github.io/pcgr/articles/running.html#example-run) - Learn more about: 1. Details regarding [PCGR input files](https://sigven.github.io/pcgr/articles/input.md), and how they should be formatted 2. Configuration of [key settings](https://sigven.github.io/pcgr/articles/running.md) 3. The types and contents of [PCGR output files](https://sigven.github.io/pcgr/articles/output.md) 4. [Variant classifications implemented in PCGR](https://sigven.github.io/pcgr/articles/variant_classification.md) 5. [Primary tumor sites used in PCGR](https://sigven.github.io/pcgr/articles/primary_tumor_sites.md) 6. The list of [gene and variant annotation resources](https://sigven.github.io/pcgr/articles/annotation_resources.md) used in PCGR annotation - [Frequently asked questions (FAQ)](https://sigven.github.io/pcgr/articles/faq.md) ## Citation If you use PCGR or CPSR, please cite our publications: Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Myklebost, and Eivind Hovig. **Personal Cancer Genome Reporter: variant interpretation report for precision oncology** (2017). *Bioinformatics*. 34(10):1778–1780. [doi.org/10.1093/bioinformatics/btx817](https://doi.org/10.1093/bioinformatics/btx817) Sigve Nakken, Vladislav Saveliev, Oliver Hofmann, Pål Møller, Ola Myklebost, and Eivind Hovig. **Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer** (2021). *Int J Cancer*. [doi:\[10.1002/ijc.33749\](doi:%5B10.1002/ijc.33749)](https://doi.org/10.1002/ijc.33749) ## Contact sigven AT ifi.uio.no # Package index ## All functions - [`actionability_doc_note()`](https://sigven.github.io/pcgr/reference/actionability_doc_note.md) : Get documentation string for AMP/ASCO/CAP clinical actionability tiers - [`af_distribution()`](https://sigven.github.io/pcgr/reference/af_distribution.md) : Function that plots a histogram of the the variant allelic support (tumor) - [`append_alteration_name()`](https://sigven.github.io/pcgr/reference/append_alteration_name.md) : Function that appends informative alteration names to sample variants based on gene symbol, consequence and HGVS annotations - [`append_annotation_links()`](https://sigven.github.io/pcgr/reference/append_annotation_links.md) : Function that appends multiple HTML annotation links to variant identifiers e.g. COSMIC, CLINVAR, REFSEQ etc - [`append_cancer_association_ranks()`](https://sigven.github.io/pcgr/reference/append_cancer_association_ranks.md) : Function that appends cancer gene evidence links - [`append_cancer_gene_evidence()`](https://sigven.github.io/pcgr/reference/append_cancer_gene_evidence.md) : Function that appends cancer gene evidence links - [`append_dbmts_var_link()`](https://sigven.github.io/pcgr/reference/append_dbmts_var_link.md) : Function that adds miRNA target annotations (dbMTS) to genetic variant identifiers - [`append_dbnsfp_var_link()`](https://sigven.github.io/pcgr/reference/append_dbnsfp_var_link.md) : Function that assigns HTML links to dbNSFP prediction entries - [`append_drug_var_link()`](https://sigven.github.io/pcgr/reference/append_drug_var_link.md) : Function that adds link to targeted drugs (on and off-label) for a list of variants and associated targeted - [`append_gwas_citation_phenotype()`](https://sigven.github.io/pcgr/reference/append_gwas_citation_phenotype.md) : Function that adds GWAS citation/phenotype to GWAS hit found through PCGR annotation - [`append_oncogenicity_docs()`](https://sigven.github.io/pcgr/reference/append_oncogenicity_docs.md) : Function that adds oncogenicity documentation from codes - [`append_protein_domains()`](https://sigven.github.io/pcgr/reference/append_protein_domains.md) : Function that adds protein domain annotations (PFAM) for a list of variants and associated targeted - [`append_styled_cna_vclass()`](https://sigven.github.io/pcgr/reference/append_styled_cna_vclass.md) : Function that styles CNA variant classes (amplification, gain, hetdel, homdel/hemdel) with more informative names for display in PCGR reports and other outputs - [`append_targeted_drug_annotations()`](https://sigven.github.io/pcgr/reference/append_targeted_drug_annotations.md) : Function that adds link to targeted drugs (on and off-label) for a list of variants and associated targeted - [`append_tcga_var_link()`](https://sigven.github.io/pcgr/reference/append_tcga_var_link.md) : Function that adds TCGA annotations (cohort, frequency etc.) to variant identifiers - [`append_tfbs_annotation()`](https://sigven.github.io/pcgr/reference/append_tfbs_annotation.md) : Function that adds TFBS annotations (dbMTS) to genetic variant identifiers - [`assign_amp_asco_cap_tiers()`](https://sigven.github.io/pcgr/reference/assign_amp_asco_cap_tiers.md) : AMP/ASCO/CAP tier classification for somatic variants in cancer - [`assign_bm_tier_support_ttagnostic()`](https://sigven.github.io/pcgr/reference/assign_bm_tier_support_ttagnostic.md) : For all biomarker evidence items with specified confidence level, assign whether these are tier-defining or providing additional support - tumor-type agnostic query - [`assign_bm_tier_support_ttspecific()`](https://sigven.github.io/pcgr/reference/assign_bm_tier_support_ttspecific.md) : For all biomarker evidence items with specified confidence level, assign whether these are tier-defining or providing additional support - tumor-type specific query - [`assign_germline_popfreq_status()`](https://sigven.github.io/pcgr/reference/assign_germline_popfreq_status.md) : Function that sets gnomAD_AF_ABOVE_TOLERATED to TRUE for variants if any gnomAD population frequency exceeds max_tolerated_af - [`assign_germline_popfreq_status_old()`](https://sigven.github.io/pcgr/reference/assign_germline_popfreq_status_old.md) : Function that sets STATUS_POPFREQ_1KG_ABOVE_TOLERATED/ STATUS_POPFREQ_GNOMAD_ABOVE_TOLERATED to TRUE for variants if any population frequency exceeds max_tolerated_af - [`assign_mutation_type()`](https://sigven.github.io/pcgr/reference/assign_mutation_type.md) : Function that assigns one of six mutation types to a list of mutations - [`assign_somatic_classification()`](https://sigven.github.io/pcgr/reference/assign_somatic_classification.md) : Function that assigns a SOMATIC_CLASSIFICATION to variants based on evidence found in variant set, potentially limited by user-defined options - [`assign_somatic_germline_evidence()`](https://sigven.github.io/pcgr/reference/assign_somatic_germline_evidence.md) : Function that appends several tags denoting evidence for somatic/germline status of variants - [`assign_variant_tiers_cna()`](https://sigven.github.io/pcgr/reference/assign_variant_tiers_cna.md) : Assign tiers of clinical significance (AMP/ASCO/CAP framework) to somatic CNAs - [`assign_variant_tiers_fusion()`](https://sigven.github.io/pcgr/reference/assign_variant_tiers_fusion.md) : Assign tiers of clinical significance (AMP/ASCO/CAP framework) to RNA fusions - [`assign_variant_tiers_snv_indel()`](https://sigven.github.io/pcgr/reference/assign_variant_tiers_snv_indel.md) : Assign tiers of clinical significance (AMP/ASCO/CAP framework) to somatic SNVs/InDels - [`assign_variant_top_tiers_ttagnostic()`](https://sigven.github.io/pcgr/reference/assign_variant_top_tiers_ttagnostic.md) : Assign top tiers of clinical significance (AMP/ASCO/CAP framework) to variants based on data from biomarker evidence items (tumor-type agnostic query) - [`assign_variant_top_tiers_ttspecific()`](https://sigven.github.io/pcgr/reference/assign_variant_top_tiers_ttspecific.md) : Assign top tiers of clinical significance (AMP/ASCO/CAP framework) to variants based on data from biomarker evidence items (tumor type-specific query) - [`biomarker_evidence`](https://sigven.github.io/pcgr/reference/biomarker_evidence.md) : Fixed data types and levels for biomarker evidence items - [`bm_categories`](https://sigven.github.io/pcgr/reference/bm_categories.md) : Named list of biomarker categories used for variant classification - [`bm_evidence`](https://sigven.github.io/pcgr/reference/bm_evidence.md) : Fixed data types/categories used for biomarker evidence, e.g. 'types','levels' etc. - [`bp_junction_transcript_overlap()`](https://sigven.github.io/pcgr/reference/bp_junction_transcript_overlap.md) : Find transcripts covering given splice junction breakpoints - [`build_oncogenicity_col_defs()`](https://sigven.github.io/pcgr/reference/build_oncogenicity_col_defs.md) : Build column definitions for oncogenicity table with category-aware styling - [`build_rt_row_details()`](https://sigven.github.io/pcgr/reference/build_rt_row_details.md) : JS function for reactable row details with exclusions and card styling (Generated by Claude Opus 4.6 with some manual tweaks) - [`build_twohit_display_data()`](https://sigven.github.io/pcgr/reference/build_twohit_display_data.md) : Build display data for potential two-hit events (nested reactable) - [`callout_biomarker_scope()`](https://sigven.github.io/pcgr/reference/callout_biomarker_scope.md) : Emit the shared "biomarker types and report scope" callout note - [`cancer_phenotypes_regex`](https://sigven.github.io/pcgr/reference/cancer_phenotypes_regex.md) : Regular expression of terms indicative of cancer-related phenotypes and syndromes - [`check_common_colnames()`](https://sigven.github.io/pcgr/reference/check_common_colnames.md) : Function that checks whether a set of column names are present in two different data frames - [`check_file_exists()`](https://sigven.github.io/pcgr/reference/check_file_exists.md) : Function that checks the existence of a file - [`clean_gnomad_annotations()`](https://sigven.github.io/pcgr/reference/clean_gnomad_annotations.md) : Clean gnomAD VCF annotations - [`clean_oncokb_evidence()`](https://sigven.github.io/pcgr/reference/clean_oncokb_evidence.md) : Clean extracted evidence data from OncoKB - [`clinvar_germline_status()`](https://sigven.github.io/pcgr/reference/clinvar_germline_status.md) : Function that assigns a logical to STATUS_CLINVAR_GERMLINE based on whether a ClinVar entry of germline origin is found for a given variant (for entries in a data frame) - [`color_palette`](https://sigven.github.io/pcgr/reference/color_palette.md) : Color encodings for report elements of PCGR/CPSR - [`cosmic_sbs_signatures`](https://sigven.github.io/pcgr/reference/cosmic_sbs_signatures.md) : List of COSMIC reference mutational signatures (SBS, v3.4) - [`cosmic_somatic_status()`](https://sigven.github.io/pcgr/reference/cosmic_somatic_status.md) : Function that assigns a logical (STATUS_COSMIC) reflecting whether a variant co-incides with an entry in COSMIC (germline) - [`data_coltype_defs`](https://sigven.github.io/pcgr/reference/data_coltype_defs.md) : List of coltype definitions for input files to pcgrr (e.g. VCF-converted TSV, CNA TVS etc.) - [`dbsnp_germline_status()`](https://sigven.github.io/pcgr/reference/dbsnp_germline_status.md) : Function that assigns a logical (STATUS_DBSNP) reflecting whether a variant co-incides with an entry in dbSNP (germline) - [`detect_vcf_sample_name()`](https://sigven.github.io/pcgr/reference/detect_vcf_sample_name.md) : A function that detects whether the sample name in variant data frame is unique (as present in column name VCF_SAMPLE_ID), throws an error if multiple sample names are present for the CPSR workflow - [`df_string_replace()`](https://sigven.github.io/pcgr/reference/df_string_replace.md) : Function that performs stringr::str_replace on strings of multiple string columns of a dataframe - [`effect_prediction_algos`](https://sigven.github.io/pcgr/reference/effect_prediction_algos.md) : List of URLs for a range of variant effect prediction algorithms - [`exclude_non_chrom_variants()`](https://sigven.github.io/pcgr/reference/exclude_non_chrom_variants.md) : Function that excludes genomic aberrations from non-nuclear chromosomes - [`exonic_filter_levels`](https://sigven.github.io/pcgr/reference/exonic_filter_levels.md) : Exonic filter levels - [`export_quarto_evars()`](https://sigven.github.io/pcgr/reference/export_quarto_evars.md) : Export Quarto Environment Variables - [`expression_doc_note()`](https://sigven.github.io/pcgr/reference/expression_doc_note.md) : Get documentation string for RNA expression analysis (outlier, similarity) - [`extract_complete_annotation()`](https://sigven.github.io/pcgr/reference/extract_complete_annotation.md) : Extract mutation effect information - [`extract_diagnostic_evidence()`](https://sigven.github.io/pcgr/reference/extract_diagnostic_evidence.md) : Extract diagnostic implications from OncoKB annotation - [`extract_prognostic_evidence()`](https://sigven.github.io/pcgr/reference/extract_prognostic_evidence.md) : Extract prognostic implications from OncoKB annotation - [`extract_therapeutic_evidence()`](https://sigven.github.io/pcgr/reference/extract_therapeutic_evidence.md) : Extract therapeutic evidence items from OncoKB annotation - [`fetch_oncokb_cna_annotation()`](https://sigven.github.io/pcgr/reference/fetch_oncokb_cna_annotation.md) : Fetch OncoKB annotation for copy number alteration - [`fetch_oncokb_fusion_annotation()`](https://sigven.github.io/pcgr/reference/fetch_oncokb_fusion_annotation.md) : Fetch OncoKB annotation for gene fusion - [`fetch_oncokb_genomic_annotation()`](https://sigven.github.io/pcgr/reference/fetch_oncokb_genomic_annotation.md) : Fetch OncoKB annotation for SNV/InDel via genomic change - [`fetch_oncokb_hgvsp_annotation()`](https://sigven.github.io/pcgr/reference/fetch_oncokb_hgvsp_annotation.md) : Fetch OncoKB annotation for SNV/InDel via protein change - [`filter_maf_file()`](https://sigven.github.io/pcgr/reference/filter_maf_file.md) : Function that takes a MAF file generated with vcf2maf and filters out variants that are presumably germline (tumor-only run) - [`filter_read_support()`](https://sigven.github.io/pcgr/reference/filter_read_support.md) : Function that filters variant set on depth and allelic fraction according to settings provided by user (tumor and control) - [`fusion_doc_note()`](https://sigven.github.io/pcgr/reference/fusion_doc_note.md) : Get documentation string for RNA fusion analysis - [`generate_annotation_link()`](https://sigven.github.io/pcgr/reference/generate_annotation_link.md) : A function that generates a HTML link for selected identifiers (DBSNP, COSMIC, CLINVAR, ENTREZ) - [`generate_report()`](https://sigven.github.io/pcgr/reference/generate_report.md) : Function that generates all contents of the cancer genome report (PCGR) - [`generate_report_data_expression()`](https://sigven.github.io/pcgr/reference/generate_report_data_expression.md) : Function that generates expression data for PCGR report - [`generate_report_data_fusion()`](https://sigven.github.io/pcgr/reference/generate_report_data_fusion.md) : Function that generates fusion data for PCGR report - [`generate_report_data_kataegis()`](https://sigven.github.io/pcgr/reference/generate_report_data_kataegis.md) : Function that generates data frame with potential kataegis events - [`generate_report_data_msi()`](https://sigven.github.io/pcgr/reference/generate_report_data_msi.md) : Function that generates MSI prediction data for PCGR report - [`generate_report_data_rainfall()`](https://sigven.github.io/pcgr/reference/generate_report_data_rainfall.md) : Function that generates data for rainfall plot (mutation density along genome, considering SNVs only) - [`generate_report_data_signatures()`](https://sigven.github.io/pcgr/reference/generate_report_data_signatures.md) : Function that generates mutational signatures data for PCGR report - [`generate_report_data_tmb()`](https://sigven.github.io/pcgr/reference/generate_report_data_tmb.md) : Function that reads TSV file with TMB estimates from sample - [`generate_tier_tsv()`](https://sigven.github.io/pcgr/reference/generate_tier_tsv.md) : Function that generates dense and tiered annotated variant datasets - [`germline_filter_levels`](https://sigven.github.io/pcgr/reference/germline_filter_levels.md) : Data frame with germline filtering criteria - [`get_data_versions_sheet()`](https://sigven.github.io/pcgr/reference/get_data_versions_sheet.md) : Build the DATA_VERSIONS sheet for the Excel workbook - [`get_druggable_fusion_partner()`](https://sigven.github.io/pcgr/reference/get_druggable_fusion_partner.md) : Identify druggable fusion partners - [`get_excel_sheets()`](https://sigven.github.io/pcgr/reference/get_excel_sheets.md) : Function that produces the contents of sheets for an Excel report of PCGR output - [`get_genome_obj()`](https://sigven.github.io/pcgr/reference/get_genome_obj.md) : Get BSgenome Object - [`get_oncogenic_cna_events()`](https://sigven.github.io/pcgr/reference/get_oncogenic_cna_events.md) : Get oncogenic copy number events - [`get_prevalent_site_signatures()`](https://sigven.github.io/pcgr/reference/get_prevalent_site_signatures.md) : Function that retrieves prevalent signatures for a given tumor type/primary site Data is collected from COSMIC v3.4. - [`get_settings_sheet()`](https://sigven.github.io/pcgr/reference/get_settings_sheet.md) : Build the SETTINGS sheet for the Excel workbook - [`get_tumor_only_filtering_criteria()`](https://sigven.github.io/pcgr/reference/get_tumor_only_filtering_criteria.md) : Function that generates a string with filtering criteria for callsets coming from tumor-only sequencing - [`get_valid_chromosomes()`](https://sigven.github.io/pcgr/reference/get_valid_chromosomes.md) : Checks for valid chromosome names in data frame of variants - [`grpmax_faf_nc_gnomad()`](https://sigven.github.io/pcgr/reference/grpmax_faf_nc_gnomad.md) : Function that assigns a maximum value to a variable (gnomAD_NC_FAF_GRPMAX) reflecting the filter allele frequency (GrpMAX) for a given variant in the non-cancer gnomAD subset (v3.1) - [`het_af_germline_status()`](https://sigven.github.io/pcgr/reference/het_af_germline_status.md) : Function that assigns a logical (STATUS_LIKELY_GERMLINE_HETEROZYGOUS) reflecting whether a variant is likely heterozygous (germline) - based on allelic fraction (VAF_TUMOR), presence in gnomAD and dbSNP, and no presence in TCGA and COSMIC - [`hex_to_rgba()`](https://sigven.github.io/pcgr/reference/hex_to_rgba.md) : Convert Hex Color to RGBA - [`hom_af_status()`](https://sigven.github.io/pcgr/reference/hom_af_status.md) : Function that assigns a logical (STATUS_LIKELY_GERMLINE_HOMOZYGOUS) reflecting whether a variant is likely homozygous (germline) - based on allelic fraction (VAF_TUMOR) - [`immune_celltypes`](https://sigven.github.io/pcgr/reference/immune_celltypes.md) : Data frame with immune cell types - [`init_biomarker_content()`](https://sigven.github.io/pcgr/reference/init_biomarker_content.md) : Function that initiates report element with biomarker evidence information - [`init_expression_content()`](https://sigven.github.io/pcgr/reference/init_expression_content.md) : Function that initiates report element with expression information - [`init_fusion_content()`](https://sigven.github.io/pcgr/reference/init_fusion_content.md) : Function that initiates report element with fusion information - [`init_germline_content()`](https://sigven.github.io/pcgr/reference/init_germline_content.md) : Function that initiates report element with germline variant information (CPSR) - [`init_kataegis_content()`](https://sigven.github.io/pcgr/reference/init_kataegis_content.md) : Function that initiates report element with kataegis information - [`init_msi_content()`](https://sigven.github.io/pcgr/reference/init_msi_content.md) : Function that initiates report element with MSI classification - [`init_mutsignature_content()`](https://sigven.github.io/pcgr/reference/init_mutsignature_content.md) : Function that initiates report element with mutational signatures information - [`init_rainfall_content()`](https://sigven.github.io/pcgr/reference/init_rainfall_content.md) : Function that initiates report element with rainfall information - [`init_report()`](https://sigven.github.io/pcgr/reference/init_report.md) : Function that initiates PCGR/CPSR report object - [`init_tmb_content()`](https://sigven.github.io/pcgr/reference/init_tmb_content.md) : Function that initiates report element with TMB information - [`init_tumor_only_content()`](https://sigven.github.io/pcgr/reference/init_tumor_only_content.md) : Function that initiates report element with tumor-only information - [`init_var_content()`](https://sigven.github.io/pcgr/reference/init_var_content.md) : Function that initiates report element with variant data - [`init_vstats_actionable()`](https://sigven.github.io/pcgr/reference/init_vstats_actionable.md) : Function that initiates report element with actionable variant statistics information - [`init_vstats_cna()`](https://sigven.github.io/pcgr/reference/init_vstats_cna.md) : Function that initiates CNA statistics - [`init_vstats_fusion()`](https://sigven.github.io/pcgr/reference/init_vstats_fusion.md) : Function that initiates RNA fusion statistics - [`init_vstats_snv_indel()`](https://sigven.github.io/pcgr/reference/init_vstats_snv_indel.md) : Function that initiates report element with SNV/InDel statistics information - [`kataegis_detect()`](https://sigven.github.io/pcgr/reference/kataegis_detect.md) : Function that detects kataegis events from a data frame with genomic cooordinates of mutations - [`kataegis_input()`](https://sigven.github.io/pcgr/reference/kataegis_input.md) : Function that detects kataegis events from a data frame with genomic cooordinates of mutations - [`list_of_list_to_df()`](https://sigven.github.io/pcgr/reference/list_of_list_to_df.md) : Helper function to convert list of lists to data.frame - [`load_cpsr_classified_variants()`](https://sigven.github.io/pcgr/reference/load_cpsr_classified_variants.md) : Function that reads CPSR-classified variants from a TSV file - [`load_dna_variants()`](https://sigven.github.io/pcgr/reference/load_dna_variants.md) : Function that reads and validates CNA or SNV/InDel TSV files file from PCGR/CPSR pre-report (Python) pipeline - [`load_expression_csq()`](https://sigven.github.io/pcgr/reference/load_expression_csq.md) : Load expression consequence settings - [`load_expression_outliers()`](https://sigven.github.io/pcgr/reference/load_expression_outliers.md) : Load expression outlier results - [`load_expression_similarity()`](https://sigven.github.io/pcgr/reference/load_expression_similarity.md) : Load expression similarity results - [`load_reference_data()`](https://sigven.github.io/pcgr/reference/load_reference_data.md) : Function that parses and loads reference data from files in the assembly-specific PCGR bundle directory - [`load_rna_fusions()`](https://sigven.github.io/pcgr/reference/load_rna_fusions.md) : Load RNA fusion results - [`load_somatic_cna()`](https://sigven.github.io/pcgr/reference/load_somatic_cna.md) : Function that reads and validates fully annotated CNA data (segments and genes) from PCGR pre-reporting pipeline - [`load_somatic_snv_indel()`](https://sigven.github.io/pcgr/reference/load_somatic_snv_indel.md) : Function that reads and validates an annotated somatic SNV/InDel file from PCGR pre-reporting pipeline - [`load_yaml()`](https://sigven.github.io/pcgr/reference/load_yaml.md) : Function that loads YAML data with settings and file paths to annotated molecular profiles - [`lof_doc_note()`](https://sigven.github.io/pcgr/reference/lof_doc_note.md) : Get documentation string for loss-of-function annotation - [`log4r_debug()`](https://sigven.github.io/pcgr/reference/log4r_debug.md) : Write messages to logs at a given priority level - [`log4r_fatal()`](https://sigven.github.io/pcgr/reference/log4r_fatal.md) : Write messages to logs at a given priority level - [`log4r_info()`](https://sigven.github.io/pcgr/reference/log4r_info.md) : Write messages to logs at a given priority level - [`log4r_warn()`](https://sigven.github.io/pcgr/reference/log4r_warn.md) : Write messages to logs at a given priority level - [`map_biomarker_data()`](https://sigven.github.io/pcgr/reference/map_biomarker_data.md) : Function that maps biomarker identifiers from VCF variant annotation to full biomarker data tables for display in report - [`max_af_gnomad()`](https://sigven.github.io/pcgr/reference/max_af_gnomad.md) : Function that assigns a maximum value to a variable (MAX_AF_GNOMAD) reflecting the maximum allele frequency for a given variant across gnomAD populations - [`mkdir()`](https://sigven.github.io/pcgr/reference/mkdir.md) : Create directory - [`msi_doc_note()`](https://sigven.github.io/pcgr/reference/msi_doc_note.md) : Get documentation string for MSI status prediction - [`msi_indel_fraction_plot()`](https://sigven.github.io/pcgr/reference/msi_indel_fraction_plot.md) : Function that plots the indel fraction for a given sample and contrasts this with the distribution for MSI-H/MSS samples from TCGA - [`msi_indel_load_plot()`](https://sigven.github.io/pcgr/reference/msi_indel_load_plot.md) : Function that plots the indel load for a given sample and contrasts this with the distribution for MSI-H/MSS samples from TCGA - [`mutational_signatures_doc_note()`](https://sigven.github.io/pcgr/reference/mutational_signatures_doc_note.md) : Get documentation string for mutational signatures analysis - [`oncogenicity_criteria`](https://sigven.github.io/pcgr/reference/oncogenicity_criteria.md) : Oncogenicity criteria (ClinGen/CGC/VICC) - [`oncogenicity_doc_note()`](https://sigven.github.io/pcgr/reference/oncogenicity_doc_note.md) : Get documentation string for oncogenicity annotation - [`oncokb_annotations`](https://sigven.github.io/pcgr/reference/oncokb_annotations.md) : Character vector with OncoKB annotations coming from the MafAnnotator / FusionAnnotator / CnaAnnnotator tools in the PCGR Python workflow. These annotations are used for variant classification and reporting in PCGR. - [`oncokb_base_api_url`](https://sigven.github.io/pcgr/reference/oncokb_base_api_url.md) : OncoKB base API URL - [`order_variants()`](https://sigven.github.io/pcgr/reference/order_variants.md) : Function that orders genomic aberrations according to order of chromosomes and chromosomal position - [`pkg_exists()`](https://sigven.github.io/pcgr/reference/pkg_exists.md) : Does R Package Exist - [`plot_cna_segments_absolute()`](https://sigven.github.io/pcgr/reference/plot_cna_segments_absolute.md) : Plot allele-specific copy number segments (absolute copies) - [`plot_cna_segments_relative()`](https://sigven.github.io/pcgr/reference/plot_cna_segments_relative.md) : Plot copy number segments (relative log2 fold change) - [`plot_filtering_stats_exonic()`](https://sigven.github.io/pcgr/reference/plot_filtering_stats_exonic.md) : Function that generates a pie chart for exonic/non-exonic variant statistics (for callsets coming from tumor-only sequencing) - [`plot_filtering_stats_germline()`](https://sigven.github.io/pcgr/reference/plot_filtering_stats_germline.md) : Function that generates a pie chart for germline filtering statistics for callsets coming from tumor-only sequencing - [`plot_signature_contributions()`](https://sigven.github.io/pcgr/reference/plot_signature_contributions.md) : Function that makes plots of mutational signature contributions in a given sample (both ggplot and plotly) - [`plot_tmb_primary_site_tcga()`](https://sigven.github.io/pcgr/reference/plot_tmb_primary_site_tcga.md) : Function that makes a plot with TMB boxplots for reference cohorts, highlighting the TMB estimate for a given sample and the cohort/primary site of interest - [`plot_value_boxes()`](https://sigven.github.io/pcgr/reference/plot_value_boxes.md) : Function that plots four value boxes with the most important findings in the cancer genome - [`plotly_pie_chart()`](https://sigven.github.io/pcgr/reference/plotly_pie_chart.md) : Plotly Pie Chart - variant statistics - [`pon_status()`](https://sigven.github.io/pcgr/reference/pon_status.md) : Function that assigns a logical (STATUS_PON) reflecting whether a variant is co-inciding with a variant present in a panel-of-normals database (PANEL_OF_NORMALS column is TRUE) - [`popmax_af_gnomad()`](https://sigven.github.io/pcgr/reference/popmax_af_gnomad.md) : Function that assigns a maximum value to a variable (gnomAD_AF_POPMAX) reflecting the maximum allele frequency for a given variant across gnomAD populations - [`predict_msi_status()`](https://sigven.github.io/pcgr/reference/predict_msi_status.md) : Function that predicts MSI status based on fraction of indels among calls - [`prep_actble_display_tbl()`](https://sigven.github.io/pcgr/reference/prep_actble_display_tbl.md) : Function that gathers data tables on actionable variants for display in report (tier 1 + tier 2) - [`prep_diagn_display_tbl()`](https://sigven.github.io/pcgr/reference/prep_diagn_display_tbl.md) : Function that gathers data tables on diagnostic variants - [`prep_progn_display_tbl()`](https://sigven.github.io/pcgr/reference/prep_progn_display_tbl.md) : Function that gathers data tables on prognostic variants for display in report - [`process_oncokb_cna()`](https://sigven.github.io/pcgr/reference/process_oncokb_cna.md) : Process OncoKB CNA output file and fetch complete annotations - [`process_oncokb_fusion()`](https://sigven.github.io/pcgr/reference/process_oncokb_fusion.md) : Process OncoKB fusion output file and fetch complete annotations - [`process_oncokb_maf()`](https://sigven.github.io/pcgr/reference/process_oncokb_maf.md) : Process OncoKB MAF output files (both HGVSp and HGVSg) and fetch complete annotations - [`remove_cols_from_df()`](https://sigven.github.io/pcgr/reference/remove_cols_from_df.md) : Function that removes column(s) from data frame - [`render_actble_bm_table()`](https://sigven.github.io/pcgr/reference/render_actble_bm_table.md) : Build biomarker reactable with category-aware styling Combines tier 1 and tier 2 records in one table. Header uses tier 1 color; THERAPY_MATCH cell background reflects the row's tier (1 or 2). - [`render_alteration_cell()`](https://sigven.github.io/pcgr/reference/render_alteration_cell.md) : Render sample alteration with confidence icon Uses filled circle + bold for high confidence, hollow circle + muted for medium confidence - [`render_alteration_clinvar_style()`](https://sigven.github.io/pcgr/reference/render_alteration_clinvar_style.md) : Style alteration cell background based on ClinVar classification (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_bar_cell()`](https://sigven.github.io/pcgr/reference/render_bar_cell.md) : Render a value between 0 and 1 as a horizontal bar (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_diagn_bm_table()`](https://sigven.github.io/pcgr/reference/render_diagn_bm_table.md) : Build biomarker reactable with category-aware styling Combines tier 1 and tier 2 records in one table. Header uses tier 1 color; THERAPY_MATCH cell background reflects the row's tier (1 or 2). - [`render_diagnosis()`](https://sigven.github.io/pcgr/reference/render_diagnosis.md) : Render diagnosis cell with background color based on actionability tier (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_evidence_desc_cell()`](https://sigven.github.io/pcgr/reference/render_evidence_desc_cell.md) : Render evidence description with truncation and tooltip (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_evidence_level_cell()`](https://sigven.github.io/pcgr/reference/render_evidence_level_cell.md) : Render evidence level badge (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_oncogenicity_cell()`](https://sigven.github.io/pcgr/reference/render_oncogenicity_cell.md) : Style oncogenicity cell background based on value (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_progn_bm_table()`](https://sigven.github.io/pcgr/reference/render_progn_bm_table.md) : Build biomarker reactable with category-aware styling Combines tier 1 and tier 2 records in one table. Header uses tier 1 color; THERAPY_MATCH cell background reflects the row's tier (1 or 2). - [`render_prognostic_outcome()`](https://sigven.github.io/pcgr/reference/render_prognostic_outcome.md) : Render prognostic outcome cell with background color based on actionability tier (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_source_logos()`](https://sigven.github.io/pcgr/reference/render_source_logos.md) : Render one or more source logos from a pipe-separated string (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_symbol_assoc_style()`](https://sigven.github.io/pcgr/reference/render_symbol_assoc_style.md) : Style alteration cell background based on cancer association rank (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_therapy_style()`](https://sigven.github.io/pcgr/reference/render_therapy_style.md) : Render therapy match cell with background color based on actionability tier (Generated by Claude Opus 4.6 with some manual tweaks) - [`render_tier_cell()`](https://sigven.github.io/pcgr/reference/render_tier_cell.md) : Render actionability tier as a styled badge with tier-specific colors - [`rna_fusion_recurrence_mitdb()`](https://sigven.github.io/pcgr/reference/rna_fusion_recurrence_mitdb.md) : Function that checks for recurrence of RNA fusions in Mitelman database and annotates with clinical and cytogenetic features - [`rt_theme()`](https://sigven.github.io/pcgr/reference/rt_theme.md) : Predefined reactable theme for PCGR/CPSR tables (Generated by Claude Opus 4.6 with some manual tweaks) - [`sort_chromosomal_segments()`](https://sigven.github.io/pcgr/reference/sort_chromosomal_segments.md) : Function that sorts chromosomal segments according to chromosome and chromosomal start/end position - [`stats_report_cna()`](https://sigven.github.io/pcgr/reference/stats_report_cna.md) : Function that computes various variant statistics for CNAs from a callset object - [`stats_report_fusion()`](https://sigven.github.io/pcgr/reference/stats_report_fusion.md) : Function that computes various variant statistics for fusions from a callset object - [`stats_report_germline()`](https://sigven.github.io/pcgr/reference/stats_report_germline.md) : Function that generate stats for a germline variant callset, including number of variants and number of variants with evidence items for each BM evidence type - [`stats_report_snv_indel()`](https://sigven.github.io/pcgr/reference/stats_report_snv_indel.md) : Function that computes various variant statistics for SNVs/InDels from a callset object - [`stats_type_snv_indel()`](https://sigven.github.io/pcgr/reference/stats_type_snv_indel.md) : Function that computes various variant statistics from a data frame with variant records - [`strip_html()`](https://sigven.github.io/pcgr/reference/strip_html.md) : Strip HTML tags - [`sync_biomarker_evidence()`](https://sigven.github.io/pcgr/reference/sync_biomarker_evidence.md) : Re-synchronize biomarker evidence items/classifications with a (possibly further-filtered) variant set - [`table_display_cols`](https://sigven.github.io/pcgr/reference/table_display_cols.md) : HTML Table display columns - [`tcga_cohorts`](https://sigven.github.io/pcgr/reference/tcga_cohorts.md) : Data frame with all TCGA cohorts - [`tcga_somatic_status()`](https://sigven.github.io/pcgr/reference/tcga_somatic_status.md) : Function that assigns a logical (STATUS_TCGA_SOMATIC) reflecting whether a variant co-incides with an entry in TCGA (somatic) - [`tier_af_distribution()`](https://sigven.github.io/pcgr/reference/tier_af_distribution.md) : Function that plots a histogram of the the variant allelic support (tumor) - grouped by tiers - [`tmb_doc_note()`](https://sigven.github.io/pcgr/reference/tmb_doc_note.md) : Get documentation string for tumor mutational burden (TMB) annotation - [`tsv_cols`](https://sigven.github.io/pcgr/reference/tsv_cols.md) : TSV columns - [`tumor_sites`](https://sigven.github.io/pcgr/reference/tumor_sites.md) : Character vector of tumor site names used in PCGR/CPSR reports - [`twohit_doc_note()`](https://sigven.github.io/pcgr/reference/twohit_doc_note.md) : Get documentation string for two-hit detection & VAF consistency assessment - [`update_report()`](https://sigven.github.io/pcgr/reference/update_report.md) : Function that updates a PCGR/CPSR report object structure - [`vaf_plot()`](https://sigven.github.io/pcgr/reference/vaf_plot.md) : Function that generates a VAF distribution plot for a given PCGR report object - [`variant_db_url`](https://sigven.github.io/pcgr/reference/variant_db_url.md) : List of URLS and variant identifiers for variant/gene/protein domain databases - [`write_processed_vcf()`](https://sigven.github.io/pcgr/reference/write_processed_vcf.md) : Function that writes a VCF intended for mutational signature analysis - [`write_report_excel()`](https://sigven.github.io/pcgr/reference/write_report_excel.md) : Function that writes key datasets of PCGR object to an Excel workbook - [`write_report_html()`](https://sigven.github.io/pcgr/reference/write_report_html.md) : Function that writes contents of PCGR object to an HTML report (quarto-based) - [`write_report_tsv()`](https://sigven.github.io/pcgr/reference/write_report_tsv.md) : Function that writes contents of PCGR object to various output formats (Rmarkdown/flexdashboard HTML reports, JSON, tab-separated etc) # Articles ### All vignettes - [Annotation resources](https://sigven.github.io/pcgr/articles/annotation_resources.md): - [Changelog](https://sigven.github.io/pcgr/articles/CHANGELOG.md): - [Developers](https://sigven.github.io/pcgr/articles/developers.md): - [FAQ](https://sigven.github.io/pcgr/articles/faq.md): - [Input files](https://sigven.github.io/pcgr/articles/input.md): - [Installation](https://sigven.github.io/pcgr/articles/installation.md): - [Output files](https://sigven.github.io/pcgr/articles/output.md): - [Primary Tumor Sites](https://sigven.github.io/pcgr/articles/primary_tumor_sites.md): - [Running](https://sigven.github.io/pcgr/articles/running.md): - [Variant classification](https://sigven.github.io/pcgr/articles/variant_classification.md):