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acmg
Scores and documentation of ACMG evidence criteria used for variant classification
in CPSR
append_cpg_properties()
Function that appends mechanism-of-inheritance (MOI) and mechanism
of disease (MOD) annotations to cancer predisposition genes (cpg's),
as well as estimated fractions of truncation vs. non-truncating variants
etc per predisposition gene (from ClinVar)
assign_classification()
Function that assigns final pathogenicity classification (B, LB, VUS, P, LP)
based on accumulated scores from different ACMG criteria and pre-defined
cutoffs (calibrated against ClinVar)
assign_pathogenicity_evidence()
Function that assigns variant pathogenicity evidence based on ACMG guidelines
assign_variant_tiers()
Function that assign variants to different tiers for
prioritization of germline variants
check_variant2cancer_phenotype()
Function that retrieves variants in cancer predisposition genes linked
to cancer-related conditions according to ClinVar
col_format_output
Format of CPSR output data frames (HTML, TSV)
generate_cpsr_report()
Function that generates variant predisposition report - CPSR
get_insilico_prediction_statistics()
Function that counts insilico predictions of variant effects
(i.e. damaging/tolerated) from dbNSFP
get_max_rows_pr_datatable()
Function that gets the maximum number of rows across different
tier data frames in CPSR report
load_germline_snv_indel()
Function that reads and validates an annotated germline SNV/InDel
file from CPSR pre-reporting pipeline
plot_summary_statistics()
Function that makes a piechart showing the number of variants at
each significance level
plot_virtual_panels()
Function that makes a HTML display of virtual gene panel
retrieve_secondary_calls()
Function that retrieves variants in genes recommended for secondary
findings
write_cpsr_output()
Function that writes contents of CPSR report object to various output formats
(quarto HTML reports, TSV, XLSX workbooks etc)
