Added parentage functions by josuechinchilla · Pull Request #59 · Breeding-Insight/BIGr

josuechinchilla · 2026-04-22T17:44:46Z

Added 2 parentage functions along with test files for them. updated imporFrom statemetns for ped_check

Development

Copilot

Pull request overview

This PR updates package exports/imports to support new pedigree/parentage-related functionality, including exposing validate_pedigree() and tightening check_ped() dependency declarations.

Changes:

Export validate_pedigree() and add its data.table roxygen imports.
Replace broad @import directives in check_ped() with more specific @importFrom entries.
Regenerate/update NAMESPACE accordingly (including adding tools::file_path_sans_ext and janitor::clean_names imports).

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
R/validate_pedigree.R	Adds `@importFrom data.table ...` for `validate_pedigree()` and ensures it’s exported.
R/check_ped.R	Switches roxygen imports to `@importFrom` for `dplyr`/`janitor` and adds `tools::file_path_sans_ext`.
NAMESPACE	Updates exports/imports to match roxygen (adds `export(validate_pedigree)`, switches janitor import style, adds additional `dplyr` imports).

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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 3 out of 3 changed files in this pull request and generated 2 comments.

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codecov · 2026-04-22T18:13:49Z

Codecov Report

❌ Patch coverage is 54.51713% with 146 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.96%. Comparing base (ccc0952) to head (f798362).

Files with missing lines	Patch %	Lines
R/find_parentage.R	16.45%	66 Missing ⚠️
R/validate_pedigree.R	32.63%	64 Missing ⚠️
R/check_ped.R	89.11%	16 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #59      +/-   ##
===============================================
- Coverage        81.53%   78.96%   -2.58%     
===============================================
  Files               23       23              
  Lines             2616     2814     +198     
===============================================
+ Hits              2133     2222      +89     
- Misses             483      592     +109

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…ement for documentation on check_ped

…and to plot results.

Copilot

Pull request overview

Copilot reviewed 12 out of 13 changed files in this pull request and generated 6 comments.

Comments suppressed due to low confidence (1)

man/validate_pedigree.Rd:90

The function always writes corrected_pedigree.txt to the working directory (even when write_results = FALSE), but this side-effect isn’t documented here. Please document this output file (including when it’s written and how it relates to write_results) so users aren’t surprised by unexpected files in their working directory.

\description{
Validates parent-offspring trios by calculating Mendelian error rates from
SNP genotype data. Identifies incorrect parentage assignments and suggests
best-matching replacements. If a list of founders is supplied, trios that
are declared founders (both parents coded as 0) are preserved unchanged
with no recommendations. Trios removed due to missing genotype data are
retained in the output with a NO_GENOTYPE_DATA status.
}

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Copilot

Pull request overview

Copilot reviewed 12 out of 13 changed files in this pull request and generated 3 comments.

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Copilot

Pull request overview

Copilot reviewed 12 out of 13 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

NAMESPACE:33

NAMESPACE no longer imports janitor, and a repo-wide search shows no remaining janitor:: usage. However, DESCRIPTION still lists janitor under Imports, which will typically trigger an R CMD check NOTE about unused imports. Either remove janitor from DESCRIPTION or reintroduce an actual use/import as appropriate.

import(dplyr)
import(parallel)
import(quadprog)
import(stringr)
import(tibble)
import(tidyr)
import(vcfR)

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Copilot

Pull request overview

Copilot reviewed 12 out of 13 changed files in this pull request and generated 2 comments.

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Copilot

Pull request overview

Copilot reviewed 12 out of 19 changed files in this pull request and generated 7 comments.

Files not reviewed (6)

man/allele_freq_poly.Rd: Language not supported
man/check_ped.Rd: Language not supported
man/find_parentage.Rd: Language not supported
man/imputation_concordance.Rd: Language not supported
man/solve_composition_poly.Rd: Language not supported
man/validate_pedigree.Rd: Language not supported

Comments suppressed due to low confidence (1)

DESCRIPTION:66

janitor remains listed under Imports, but there are no longer any janitor:: (or clean_names) usages in the R sources. This makes janitor an unnecessary hard dependency; consider removing it from DESCRIPTION Imports if it's truly unused.

Imports: 
    parallel,
    dplyr,
    Rdpack (>= 0.7),
    readr (>= 2.1.5),
    reshape2 (>= 1.4.4),
    rlang,
    tidyr (>= 1.3.1),
    vcfR (>= 1.15.0),
    Rsamtools,
    Biostrings,
    pwalign,
    janitor,
    quadprog,
    tibble,
    stringr,
    data.table
Suggests:

…documentations

… or file paths, updated documentation and test files

Copilot

Pull request overview

Copilot reviewed 13 out of 20 changed files in this pull request and generated 4 comments.

Files not reviewed (6)

man/allele_freq_poly.Rd: Language not supported
man/check_ped.Rd: Language not supported
man/find_parentage.Rd: Language not supported
man/imputation_concordance.Rd: Language not supported
man/solve_composition_poly.Rd: Language not supported
man/validate_pedigree.Rd: Language not supported

+importFrom(ggplot2,aes)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_minimal)


  }

-  missing_parents <- distinct(missing_parents)
+  missing_parents <- dplyr::distinct(missing_parents)


+      id                  = progeny_ids,
+      male_parent         = NA_character_,
+      female_parent       = NA_character_,
+      mendelian_error_pct = NA_character_,


+        ggplot2::geom_vline(xintercept = error_threshold,
+                            linetype = "dashed", color = "black", linewidth = 1) +
+        ggplot2::scale_x_continuous(breaks = seq(0, 100, by = 5)) +
+        ggplot2::scale_y_continuous(breaks = seq(0, 10000, by = 5)) +


josuechinchilla and others added 3 commits April 22, 2026 13:27

Merge pull request #58 from Breeding-Insight/development

f590dad

Development

corrected importFrom statement in parentage functions and ped_check

20d2764

updated NAMESPACE to reflect updated importFrom statements

f2d3f40

josuechinchilla requested review from alex-sandercock and Copilot April 22, 2026 17:44

Copilot started reviewing on behalf of josuechinchilla April 22, 2026 17:45 View session

alex-sandercock added the in_progress not ready to merge label Apr 22, 2026

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Comment thread R/check_ped.R Outdated

Update R/check_ped.R

c1fe543

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

josuechinchilla requested a review from Copilot April 22, 2026 17:58

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Comment thread R/validate_pedigree.R Outdated

Comment thread R/check_ped.R Outdated

josuechinchilla removed the request for review from alex-sandercock April 23, 2026 20:13

josue.chinchilla added 3 commits April 24, 2026 13:52

updated error handling and reporting for check_ped, Also major improv…

0a13483

…ement for documentation on check_ped

updated error handling and reporting for check_ped

9bbc507

updated parentage functions to work allow user to display NA or not, …

f798362

…and to plot results.

josuechinchilla requested a review from Copilot April 27, 2026 18:33

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Comment thread R/find_parentage.R Outdated

Comment thread R/find_parentage.R

Comment thread R/find_parentage.R Outdated

Comment thread R/check_ped.R Outdated

Comment thread R/check_ped.R Outdated

Comment thread R/validate_pedigree.R Outdated

josuechinchilla requested a review from Copilot April 27, 2026 18:39

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Comment thread NAMESPACE

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Comment thread man/validate_pedigree.Rd Outdated

Made edits suggested by autopilot

03725d8

josuechinchilla requested a review from Copilot April 27, 2026 19:10

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added edits suggested by copilot

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josuechinchilla requested a review from Copilot April 27, 2026 19:45

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Comment thread R/check_ped.R

Comment thread R/find_parentage.R Outdated

josuechinchilla requested review from alex-sandercock April 27, 2026 19:52

josue.chinchilla added 4 commits April 28, 2026 11:15

modified default params

977e070

Added authors fror functions and made headers concise

5db5fa2

staged comments for next push

6b84e18

removed zip option and added specific correction arguments

4eb79bb

alex-sandercock requested a review from Copilot May 20, 2026 20:26

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Comment thread tests/testthat/test-check_ped.R Outdated

Comment thread man/check_ped.Rd

Comment thread NAMESPACE

Comment thread R/imputation_concordance.R

josue.chinchilla added 4 commits May 22, 2026 07:36

finalzied refactoring according to CRAN standards

1fb19d0

Updated functions and descriptions to be CRAN compliant and updatede …

65d48fd

…documentations

updated parentage functions to standardize inputs and outputs

9b16038

updated functions to work as a workflow accepting inputs from objects…

26bae5f

… or file paths, updated documentation and test files

josuechinchilla requested a review from Copilot May 26, 2026 20:36

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