Package index
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gt4_binary_path() - Locate a bundled GenomeTester4 executable
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gt4_run()gmer_counter()glistcompare()glistmaker()glistquery()gassembler()gmer_caller() - Run GenomeTester4 binaries with processx
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gt4_run_script()generate_vcf()katk2vcf()make_intersection()make_union()collate_repeats()find_regions()filter_collated()filter_final()unique_repeats() - Run GenomeTester4 Perl scripts with processx
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gt4_script_path() - Locate a bundled GenomeTester4 Perl script
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niptmer_bind_count_table() - Append sample count rows to a NIPTmer reference count table
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niptmer_build_reference_lists() - Build unique per-chromosome reference k-mer lists
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niptmer_compute_coverage() - Compute per-sample coverage from count matrix
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niptmer_count_sample_list() - Count a sample list against chromosome NIPTmer lists
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niptmer_diagnose_controls() - Diagnose control-group outliers using leave-one-out chromosome z-scores
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niptmer_filter_controls() - Filter control-group outliers
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niptmer_interpret() - Interpret a NIPTmer score row into a compact call
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niptmer_make_sample_list() - Build a sample k-mer list for NIPTmer
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niptmer_match_qc() - Compute Match QC score for one sample
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niptmer_match_qc_threshold() - Estimate Match QC threshold from a control set
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niptmer_prepare_counts() - Prepare NIPTmer count data
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niptmer_read_table() - Read a NIPTmer count table
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niptmer_ref_apply_whitelist() - Intersect a reference panel with a whitelist
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niptmer_ref_blacklist_from_bed() - Build a BED-region blacklist
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niptmer_ref_blacklist_from_vcf() - Build a polymorphism blacklist from population VCF files
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niptmer_ref_build() - Build a reference panel using population-specific filters
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niptmer_ref_import() - Import an existing per-chromosome reference panel
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niptmer_ref_profile_ulcwgs() - Suggested defaults for ULCWGS reference-building
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niptmer_ref_qc() - Summarize reference panel list sizes and GC content
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niptmer_ref_stability_whitelist() - Build a population stability whitelist from euploid controls
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niptmer_ref_subtract_blacklists() - Subtract one or more blacklist lists from a reference panel
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niptmer_run_sample() - Run the file-oriented NIPTmer sample workflow
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niptmer_score_samples() - Run the NIPTmer regression model on count data
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niptmer_select_reference_subset() - Select best-matching control subset for a sample
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niptmer_write_xya() - Write legacy NIPTmer XYA interpretation output
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niptmer_write_zscore() - Write legacy NIPTmer z-score output