API for grailbio/conta
Detect cross-contamination
| Global functions | |
|---|---|
| add_chunks | Source code |
| add_error_rates | Source code |
| annotate_and_filter | Source code |
| avg_llr_cont | Source code |
| avg_llr_loh | Source code |
| bayesian_genotype | Source code |
| bounded_freqs | Source code |
| calculate_error_model | Source code |
| calculate_ranked_predictions | Source code |
| chr_stats | Source code |
| combine_counts | Source code |
| conta_ethnicity | Source code |
| conta_llr | Source code |
| conta_main | Source code |
| conta_source | Source code |
| conta_swap | Source code |
| conta_threshold | Source code |
| dbetabinom | Source code |
| empty_result | Source code |
| exclude_high_loh_regions | Source code |
| factorize_chroms | Source code |
| fail_test | Source code |
| filter_data | Source code |
| filter_gt_file | Source code |
| fit_sens_by_conta_level | Source code |
| genotype_concordance | Source code |
| get_bases | Source code |
| get_ethnicity_priors | Source code |
| get_exp_cf | Source code |
| get_genomic_seq | Source code |
| get_genomic_seqs | Source code |
| get_genotype_concordance | Source code |
| get_gt_likelihoods | Source code |
| get_initial_loh_range | Source code |
| get_initial_range | Source code |
| get_lr | Source code |
| get_per_bin_loh | Source code |
| get_pregnancy_call | Source code |
| get_s3_folders | Source code |
| get_sample_name | Source code |
| get_sex_call | Source code |
| get_snp_intersection | Source code |
| get_snp_likelihoods | Source code |
| get_source_llr | Source code |
| intersect_snps | Source code |
| is_compatible_context | Source code |
| l_loh | Source code |
| ldbetabinom | Source code |
| llr_cont | Source code |
| llr_cont_all | Source code |
| llr_loh | Source code |
| llr_loh_all | Source code |
| load_conta_file | Source code |
| log_lr | Source code |
| make_roc_plot_by_conta_level | Source code |
| nloh | Source code |
| optimize_after_grid | Source code |
| optimize_likelihood | Source code |
| parse_field | Source code |
| pg | Source code |
| pg2 | Source code |
| plot_avg_llr_by_conta | Source code |
| plot_lr | Source code |
| plot_lr_per_bin | Source code |
| plot_max_likelihood | Source code |
| plot_ranked_predictions_per_chromosome | Source code |
| plot_vfn_cp | Source code |
| prep_1000g_vcf_af | Source code |
| ratio_and_counts | Source code |
| read_and_prep | Source code |
| read_data_table | Source code |
| read_gt_file | Source code |
| read_sim_results | Source code |
| read_vcf_dt | Source code |
| sens_spec_by_level | Source code |
| set_numeric_chrs | Source code |
| sim_conta | Source code |
| sim_data_to_roc | Source code |
| simulate_loh_conta | Source code |
| ssig | Source code |
| thresholds_by_sens_spec | Source code |
| update_context | Source code |
| write_data_table | Source code |
| write_gt_file | Source code |
