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>

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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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Pull request overview

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

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

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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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Pull request overview

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

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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

…ring genotype matrices for comparisons. updated test file to accomodate nw arguments

Copilot

Pull request overview

Copilot reviewed 13 out of 20 changed files in this pull request and generated 5 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

+    } else if (decision %in% c("remove_both",
+                               "low_markers_remove_both",
+                               "low_markers_remove_male_parent",
+                               "low_markers_remove_female_parent")) {
+      if (grepl("male",   decision))
+        data.table::set(corrected_pedigree, row_idx, "male_parent",   "0")
+      if (grepl("female", decision))
+        data.table::set(corrected_pedigree, row_idx, "female_parent", "0")
+      if (decision %in% c("low_markers_remove_both", "remove_both")) {
+        data.table::set(corrected_pedigree, row_idx, "male_parent",   "0")
+        data.table::set(corrected_pedigree, row_idx, "female_parent", "0")
+      }
    }


  show_ties = TRUE,
  allow_selfing = TRUE,
  verbose = TRUE,
-  write_txt = TRUE
+  plot_results = TRUE
 )
 }
 \arguments{
-\item{genotypes_file}{Path to a TSV/CSV/TXT file containing genotype data.
-Must include an 'ID' column followed by marker columns coded as 0, 1, 2
-(allele dosage).}
+\item{genotypes_file}{Path to a TSV/CSV/TXT file, OR a data.frame /
+data.table with an 'id' column followed by marker columns coded as 0, 1, 2.}

-\item{parents_file}{Path to a TSV/CSV/TXT file listing candidate parent IDs.
-Must include an 'ID' column. An optional 'Sex' column with values
-'M' (male parent), 'F' (female parent), or 'A' (ambiguous) determines
-which parents are tested for each role. If absent, all parents are treated
-as ambiguous.}
+\item{parents_file}{Path to a TSV/CSV/TXT file, OR a data.frame /
+data.table with an 'id' column and an optional 'sex' column
+('M', 'F', or 'A'). If absent, all parents are treated as ambiguous.}

-\item{progeny_file}{Path to a TSV/CSV/TXT file listing progeny IDs to assign.
-Must include an 'ID' column.}
+\item{progeny_file}{Path to a TSV/CSV/TXT file, OR a data.frame /
+data.table with an 'id' column.}

-\item{method}{Character. Parentage assignment method. One of:
-\itemize{
-\item \code{"best_male_parent"}  — finds the best male parent for each
-progeny using homozygous mismatch rate.
-\item \code{"best_female_parent"} — finds the best female parent for each
-progeny using homozygous mismatch rate.
-\item \code{"best_match"} — finds the single best parent (either sex)
-using homozygous mismatch rate.
-\item \code{"best_pair"}  — finds the best male-female parent pair for
-each progeny using full Mendelian error rate (default).
-}}
+\item{method}{Character. One of \code{"best_male_parent"},
+\code{"best_female_parent"}, \code{"best_match"}, or
+\code{"best_pair"} (default).}

-\item{min_markers}{Integer. Minimum number of non-missing markers required
-to report a parentage assignment. Progeny-parent comparisons with fewer
-markers are flagged as \code{LOW_MARKERS} and no assignment is made
-(default: \code{10}).}
+\item{min_markers}{Integer. Minimum markers required; fewer flags
+\code{low_markers} (default: \code{10}).}

-\item{error_threshold}{Numeric. Maximum mismatch percentage to report a
-parentage assignment as confident. Assignments above this threshold are
-flagged as \code{HIGH_ERROR} in the \code{Assignment_Status} column
-(default: \code{5.0}). Must be between 0 and 100.}
+\item{error_threshold}{Numeric. Maximum mismatch percentage; exceeded values
+flag \code{high_error} (default: \code{5.0}). Must be between 0 and 100.}

-\item{show_ties}{Logical. If \code{TRUE}, all tied best pairs (after
-tie-breaking by maximum markers tested) are reported as additional columns
-(\code{Male_Parent_1}, \code{Male_Parent_2}, etc.) when
-\code{method = "best_pair"}. The base columns (\code{Male_Parent},
-\code{Female_Parent}, etc.) are always populated with the top result.
-If \code{FALSE}, only one tied pair is reported with a warning.
-Default is \code{TRUE}.}
+\item{show_ties}{Logical. If \code{TRUE}, tied best pairs are appended as
+suffix columns. Default is \code{TRUE}.}

-\item{allow_selfing}{Logical. If \code{FALSE}, male-female parent pairs where
-both IDs are identical are excluded when \code{method = "best_pair"}.
-Default is \code{TRUE}.}
+\item{allow_selfing}{Logical. If \code{FALSE}, pairs with identical male and
+female parent IDs are excluded. Default is \code{TRUE}.}

-\item{verbose}{Logical. If \code{TRUE}, prints progress messages, summary
-statistics, and the results table to the console. Default is \code{TRUE}.}
+\item{verbose}{Logical. If \code{TRUE}, prints progress and summary.
+Default is \code{TRUE}.}

-\item{write_txt}{Logical. If \code{TRUE}, writes results to
-\code{parentage_results_dt.txt} in the working directory. Default is
-\code{TRUE}.}
+\item{plot_results}{Logical. If \code{TRUE}, plots the Mendelian error
+distribution. Requires \code{ggplot2}. Default is \code{TRUE}.}
 }


+        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)) +


+      plot_df$plot_status <- dplyr::case_when(
+        plot_df$recommended_correction %in% c("none", "keep_both",
+                                              "low_markers_keep_both")               ~ "pass",
+        plot_df$recommended_correction %in% c("remove_male_parent",
+                                              "remove_female_parent",
+                                              "low_markers_remove_male_parent",
+                                              "low_markers_remove_female_parent")    ~ "fail_one_parent",
+        plot_df$recommended_correction %in% c("remove_both",
+                                              "low_markers_remove_both")             ~ "fail_both_parents",
+        TRUE                                                                           ~ "other"
+      )


 library(testthat)
 library(data.table)
-
+set.seed(101919)


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

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Update R/check_ped.R

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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.

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Made edits suggested by autopilot

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added edits suggested by copilot

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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

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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

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Comment thread NAMESPACE

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Comment thread R/find_parentage.R

Comment thread R/find_parentage.R

updated find_parentage to exlcude self comparison and fix bug of orde…

7e34dfe

…ring genotype matrices for comparisons. updated test file to accomodate nw arguments

josuechinchilla requested a review from Copilot May 29, 2026 16:36

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codecov Bot commented Apr 22, 2026 •

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