Function reference
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EFFECT_ABBREVIATIONS - Abbreviations for SV effects
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abbreviate_effect() - Abbreviate SV Effects
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af_summary() - umccrise AF summary
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bcftools_stats_plot() - Parse bcftools stats File
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cancer_rmd() - Generate UMCCR Cancer Report
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count_pieces() - Count Number of Parts in a String
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date_log() - Print current timestamp for logging
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dragen_hrd() - Parse DRAGEN HRD File
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get_oncokb_genes() - Get OncoKB Genes From Somewhere
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hrd_results_tabs() - HRDetect and CHORD Summary Table
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is_vcf() - Does the input file look like a VCF?
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mkdir() - Create directory
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pkg_exists() - Does R Package Exist
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plot_bnd_sr_pr_tot_hist() - Histogram for SR, PR and SR + PR for BNDs
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plot_bnd_sr_pr_tot_lines() - Line plot for SR, PR and SR + PR for BNDs
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process_cnv_tsv() - Process CNV TSV
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process_sv() - Process SV TSV
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purple_cnv_som_gene_process() - Process PURPLE CNV Gene File for UMCCRISE
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purple_cnv_som_gene_read() - Read PURPLE CNV Gene File
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purple_cnv_som_process() - Process PURPLE CNV Somatic File for UMCCRISE
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purple_cnv_som_read() - Read PURPLE CNV Somatic File
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purple_kataegis() - Get PURPLE Kataegis Regions
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purple_purity_read() - Read PURPLE Purity file
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purple_qc_read() - Read PURPLE QC file
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purple_snv_vcf_read() - Read PURPLE Somatic SNV VCF
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read_oncokb() - Read OncoKB
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session_info_kable() - Session Information Kable
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split_double_col() - Split Two-Field Column
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tsv_is_empty() - Does the TSV file contain any non-header rows?
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vcf_is_empty() - Does the VCF file contain any variants?
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virusbreakend_summary_read() - Read VIRUSBreakend Summary File
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virusbreakend_vcf_read() - Read VIRUSBreakend VCF File
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write_jsongz() - Write gzipped JSON
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write_tsvgz() - Write a data frame to a tab delimited gzipped file
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write_tsvjsongz() - Write a data frame to gzipped TSV and JSON files