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Sat 213 attempt2 for cn0
…Insight/Qploidy2 into nQuack_implementation2
…Insight/Qploidy2 into nQuack_implementation2
N quack implementation2
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Sex-chromosome parsing collapses X/Y identifiers to missing values, allowing markers from different chromosomes to be incorrectly associated with the same segment.
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What changed in this PR
Updates Qploidy2 from 1.16.1 to 1.24.0, expanding its copy-number analysis workflow with reference-based standardization, sex-chromosome support, and additional filtering and integration tools.
Changes:
- Adds sample and cluster filtering, reference-based z-scores, background removal, and safer segmentation.
- Extends HMM fitting, sex-aware karyotypes, result classification, and import/export support.
- Updates tests, API documentation, tutorials, and Claude Code setup guidance.
| File | Description |
|---|---|
| tests/testthat/test-standardization.R | Tests reference z-scores and updated summaries. |
| tests/testthat/test-re_standardize.R | Updates expected copy-number counts. |
| tests/testthat/test-karyotype.R | Adds sex-chromosome inference and plotting tests. |
| tests/testthat/test-hmm_cn.R | Expands HMM argument and windowing coverage. |
| README.md | Adds nQuack tutorial and Claude setup guidance. |
| R/zscore_segmentation.R | Adds chromosome-specific minima and segmentation safeguards. |
| R/utils.R | Whitespace-only change. |
| R/standardization.R | Adds filtering and reference-based depth normalization. |
| R/standardization_utils.R | Adds cluster thresholds and background removal. |
| R/split_mk_type.R | Classifies markers by sub-genome signal. |
| R/segre_test_cnv.R | Normalizes punctuation in comments and documentation. |
| R/prepare.R | Allows non-genotype VCF reads without GT. |
| R/plots_standardization.R | Updates theta labels and facet formatting. |
| R/plot_raw.R | Updates theta labels and model-selection defaults. |
| R/plot_karyotype.R | Supports sex chromosomes, reliability coloring, and masked calls. |
| R/pca_plot.R | Normalizes documentation punctuation. |
| R/merge_qploidy_data.R | Normalizes comments and documentation punctuation. |
| R/karyotype_notation.R | Adds sex inference and expected chromosome dosages. |
| R/install_claude_skills.R | Downloads workflow guidance into projects. |
| R/filter_hmm_CN.R | Adds quality masking and sample classification. |
| R/export_results.R | Groups summary helpers and adds MAPpoly/PennCNV interoperability. |
| R/em_hmm_cn.R | Revises emissions, priors, and single-window handling. |
| R/call_dosages.R | Updates heterozygosity defaults. |
| R/BAF_distributions.R | Updates BAF model-selection defaults. |
| NAMESPACE | Registers new exports, methods, and imports. |
| man/test_cn_segregation.Rd | Normalizes documentation punctuation. |
| man/summarize_cn_mode.Rd | Updates the documentation source pointer. |
| man/standardize.Rd | Documents new filtering options. |
| man/split_mk_type.Rd | Documents sub-genome marker classification. |
| man/simulate_cn_segregation.Rd | Normalizes documentation punctuation. |
| man/select_best_raw_model.Rd | Updates documented heterozygosity defaults. |
| man/select_best_baf_model.Rd | Updates documented model-selection defaults. |
| man/segreg_poly_cn.Rd | Normalizes documentation punctuation. |
| man/remove_background_noise.Rd | Documents background-signal filtering. |
| man/re_standardize.Rd | Documents filtering options and revised defaults. |
| man/print.count_types.Rd | Documents classification summary printing. |
| man/plot_xy_with_ploidy_guides.Rd | Normalizes documentation punctuation. |
| man/plot_tested_cn_segregation.Rd | Normalizes example notation. |
| man/plot_karyotype.Rd | Documents reliability coloring and sex chromosomes. |
| man/plot_cn_track_by_type.Rd | Documents grouped batch plot export. |
| man/plot_baf_with_ploidy_guides.Rd | Normalizes documentation punctuation. |
| man/pca_plot.Rd | Normalizes documentation punctuation. |
| man/merge_qploidy_datas.Rd | Normalizes documentation punctuation. |
| man/merge_cn_summary_with_estimates.Rd | Updates the documentation source pointer. |
| man/karyotype_notation.Rd | Documents sex-aware notation and expected dosages. |
| man/install_claude_skills.Rd | Documents workflow guidance installation. |
| man/import_penncnv_results.Rd | Documents PennCNV result import. |
| man/hmm_estimate_CN.Rd | Documents expanded HMM controls and emissions. |
| man/hmm_estimate_CN_nQuack.Rd | Documents the nQuack-based estimation route. |
| man/hmm_estimate_CN_multi.Rd | Clarifies forwarding of sex settings. |
| man/get_zscore.Rd | Documents reference-sample normalization. |
| man/get_centers.Rd | Documents minimum cluster sizes. |
| man/get_baf.Rd | Normalizes reference punctuation. |
| man/filter_hmm_CN.Rd | Documents quality thresholds and masking. |
| man/export_mappoly.Rd | Documents chromosome-level MAPpoly export. |
| man/em_hmm_cn.Rd | Documents BAF-only fitting and prior updates. |
| man/count_types.Rd | Documents ploidy classification and sex settings. |
| man/convert2nQuack.Rd | Documents standardized-BAF conversion and filtering. |
| man/compute_baf_likelihoods.Rd | Updates documented heterozygosity defaults. |
| man/compare_cn_track.Rd | Updates source pointer, colors, and confidence description. |
| man/compare_cn_track_summary.Rd | Documents multi-sample copy-number overview plots. |
| man/call_hmm_dosages.Rd | Updates documented heterozygosity defaults. |
| man/call_BAF_nQuack_dosages.Rd | Documents internal nQuack dosage assignment. |
| man/add_changepoint_windows.Rd | Documents chromosome-specific segment minima. |
| docs/BIcolors_template.css | Restyles inline code with light backgrounds. |
| DESCRIPTION | Bumps version and adds the nQuack dependency. |
| .Rbuildignore | Excludes Claude configuration and OAuth files. |
| .claude/agents/qploidy2-input-prep.md | Adds input-preparation workflow guidance. |
Review effort: Balanced
| } else if (baf_only) { | ||
| llb <- ll_baf_matrix[,k] | ||
| if(correct_scale) llb <- ifelse(n_baf > 0, llb / n_baf, 0) # n_baf == 0 would otherwise divide to NaN/Inf | ||
| llb[!is.finite(llb)] <- 0 |
| g <- dat[idx, , drop = FALSE] | ||
| row <- list( | ||
| Sample = g$Sample[1], | ||
| CN_mode = mode(g[[cn_col]]), |
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| tryCatch({ | ||
| utils::download.file(url, destfile = dest_file, quiet = TRUE) | ||
| message("Installed: ", dest_file) | ||
| installed <- c(installed, dest_file) | ||
| }, error = function(e) { | ||
| warning("Failed to download ", skill, ": ", conditionMessage(e)) | ||
| }) |
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| tbl$Sex <- ifelse(!valid, NA_character_, | ||
| ifelse(has_het == (sex_system == "XY"), "male", "female")) |
| rm_outlier = rm_outlier, | ||
| cluster_median = cluster_median) | ||
| cluster_median = cluster_median, | ||
| min_samples_by_cluster = min_samples_by_cluster) |
| # Z score | ||
| vmsg("Generating z scores", verbose = verbose, level = 0, type = ">>") | ||
| # Z-score mean/sd come from the reference samples in genos only | ||
| reference.samples <- unique(genos$SampleName) |
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| "ploidy.standardization (%d) differs from the mode of CN_call in dosages (%d). This may lead to unexpected results. ploidy.standardization is set to %d.", | ||
| ploidy.standardization, mode(hmm_CN_multi$by_marker$CN_call), mode(hmm_CN_multi$by_marker$CN_call) | ||
| )) | ||
| ploidy.standardization <- mode(hmm_CN_multi$by_marker$CN_call) | ||
| if(verbose) cat("Using ploidy.standardization:", ploidy.standardization, "\n") |
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| seg_len <- min(chr_minseglen, floor(length(z) / 2)) | ||
| if (!is.finite(seg_len) || seg_len < 1) seg_len <- 1L |
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Many changes. See NEWs.md