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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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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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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is_vcf_bpi() - BPI run on VCF
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linx_breakend_process() - Process LINX Breakend File
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linx_breakend_read() - Read LINX Breakend File
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linx_clusters_process() - Process LINX Clusters File
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linx_clusters_read() - Read LINX Clusters File
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linx_drivercatalog_process() - Process LINX Driver Catalog File
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linx_drivercatalog_read() - Read LINX Driver Catalog File
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linx_drivers_process() - Process LINX Drivers File
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linx_drivers_read() - Read LINX Drivers File
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linx_fusion_process() - Process LINX Fusion File
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linx_fusion_read() - Read LINX Fusion File
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linx_links_process() - Process LINX Links File
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linx_links_read() - Read LINX Links File
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linx_rmd() - Generate UMCCR LINX Report
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linx_svs_process() - Process LINX SVS File
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linx_svs_read() - Read LINX SVS File
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linx_viscopynumber_read() - Read LINX VisCopyNumber File
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linx_visfusion_read() - Read LINX VisFusion File
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linx_visgeneexon_read() - Read LINX VisGeneExon File
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linx_visproteindomain_read() - Read LINX VisProteinDomain File
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linx_vissegments_read() - Read LINX VisSegments File
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linx_vissvdata_read() - Read LINX VisSvData File
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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_sv() - Process Structural Variants
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purple_cnv_germ_process() - Process PURPLE CNV germline File for UMCCRISE
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purple_cnv_germ_read() - Read PURPLE CNV Germline File
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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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purple_version_read() - Read PURPLE version file
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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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umccrise_read_sv_tsv() - Read SV TSV
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vcf_is_empty() - Does the VCF file contain any variants?
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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