Corrections for DOF1/HSF1 data

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl2
-Version: 0.29-5
-Date: 2022-10-25
+Version: 0.29-7
+Date: 2022-10-29
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: Provides a set of tools to perform quantitative
     trait locus (QTL) analysis in experimental crosses. It is a

NEWS.md

@@ -1,9 +1,20 @@
-## qtl2 0.29-5 (2022-10-25)
+## qtl2 0.29-7 (2022-10-29)
+
+### Major changes
+
+- For DOF1 and HSF1, revised the results of `calc_genoprob()` for the
+  X chromosome, so that it just keeps track of the chromosome from the
+  DO/HS parent. In males, we are assuming that the DO/HS parent is the
+  mother.
 
 ### Minor changes
 
 - Add dependency on version of Rcpp (>= 1.0.7)
 
+- Revisions so that `genoprob_to_alleleprob()` to work with DOF1 and
+  HSF1. `plot_onegeno()` should also work now in these cases.
+  (Issue #140 and Issue #141)
+
 ### Bug fixes
 
 - Revised `predict_snpgeno()` to work for DOF1 and HSF1 populations.
@@ -20,6 +31,11 @@
 - Issue a warning message if founder genotypes are included but not
   used (Issue #211).
 
+- The treatment of the male X chromosome in DOF1 and HSF1 was
+  incorrect. We're now assuming that the DO or HS parent was the
+  mother in the F1 cross, in which case males will be hemizygous for
+  one of the DO/HS founder alleles.
+
 
 ## qtl2 0.28 (2021-10-11)
 

R/predict_snpgeno.R

@@ -87,7 +87,11 @@ function(cross, geno, cores=1)
 
        # ugh deal with DOF1/HSF1 specially
        if(cross$crosstype %in% c("dof1", "hsf1")) {
-           ph2[] <- 9 # one chromosome is from 9th founder
+           if(!is_x_chr[chr]) ph2[] <- 9 # one chromosome is from 9th founder
+           else {
+               if(any(is_male)) ph2[is_male,] <- ph1[is_male,,drop=FALSE]
+               if(any(!is_male)) ph2[!is_male,] <- 9
+           }
        }
 
        if(ncol(fg) != ncol(ph1) ||

R/snpprob_from_cross.R

@@ -25,6 +25,10 @@ snpprob_from_cross <-
     map <- cross$pmap
     if(is.null(map)) map <- cross$gmap
 
+    if(cross$crosstype %in% c("hsf1", "dof1")) { # if HSF1 or DOF1, drop last founder
+        cross$founder_geno <- cross$founder_geno[,-ncol(cross$founder_geno)]
+    }
+
     sdp <- calc_sdp(t(do.call("cbind", cross$founder_geno)))
 
     snpinfo <- data.frame(chr=rep(chr_names(cross), n_mar(cross)),

README.md

@@ -1,6 +1,6 @@
 ### [R/qtl2](https://kbroman.org/qtl2/)
 
-[![R build status](https://github.com/rqtl/qtl2/workflows/R-CMD-check/badge.svg)](https://github.com/rqtl/qtl2/actions)
+[![R-CMD-check](https://github.com/rqtl/qtl2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rqtl/qtl2/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/qtl2)](https://cran.r-project.org/package=qtl2)
 
 [Karl Broman](https://kbroman.org)

src/cross_dof1.cpp

@@ -23,12 +23,7 @@ const bool DOF1::check_geno(const int gen, const bool is_observed_value,
     const int n_alleles = 8;
     const int n_geno = 8;
 
-    if(!is_x_chr || is_female) { // autosome or female X
-        if(gen>= 1 && gen <= n_geno) return true;
-    }
-    else { // male X
-        if(gen>=n_geno+1 && gen <=n_geno+n_alleles) return true;
-    }
+    if(gen>= 1 && gen <= n_geno) return true;
 
     return false; // otherwise a problem
 }
@@ -56,13 +51,15 @@ const double DOF1::emit(const int obs_gen, const int true_gen, const double erro
 
     if(obs_gen==0) return 0.0; // missing
 
-    int f1;
-    if(!is_x_chr || is_female) // autosome or female X
-        f1 = founder_geno[true_gen-1];
-    else
-        f1 = founder_geno[true_gen-9];
+    int f1 = founder_geno[true_gen-1];
 
-    int f2 = founder_geno[8]; // 9th founder is the other strain
+    int f2;
+    if(is_x_chr && !is_female) {
+        f2 = f1; // assuming female DO x male 9th strain, so male is hemizygous DO chr
+    } else {
+        // autosome or female X chr
+        f2 = founder_geno[8]; // 9th founder is the other strain
+    }
 
     // treat founder hets as missing
     if(f1==2) f1 = 0;
@@ -162,30 +159,18 @@ const double DOF1::step(const int gen_left, const int gen_right, const double re
 const IntegerVector DOF1::possible_gen(const bool is_x_chr, const bool is_female,
                                        const IntegerVector& cross_info)
 {
-    int n_alleles = 8;
     int n_geno = 8;
 
-    if(is_x_chr && !is_female) { // male X chromosome
-        IntegerVector result(n_alleles);
-        for(int i=0; i<n_alleles; i++)
-            result[i] = n_geno+i+1;
-        return result;
-    }
-    else { // autosome or female X
-        IntegerVector result(n_geno);
-        for(int i=0; i<n_geno; i++)
-            result[i] = i+1;
-        return result;
-    }
+    IntegerVector result(n_geno);
+    for(int i=0; i<n_geno; i++)
+        result[i] = i+1;
+    return result;
+
 }
 
 const int DOF1::ngen(const bool is_x_chr)
 {
-    int n_alleles = 8;
-    int n_geno = 8;
-
-    if(is_x_chr) return n_geno+n_alleles;
-    return n_geno;
+    return 8;
 }
 
 const int DOF1::nalleles()
@@ -195,28 +180,14 @@ const int DOF1::nalleles()
 
 const NumericMatrix DOF1::geno2allele_matrix(const bool is_x_chr)
 {
-    const int n_alleles = 8;
     const int n_geno = 8;
 
-    if(is_x_chr) {
-        NumericMatrix result(n_geno+n_alleles, n_alleles);
-        // female X
-        for(int trueg=0; trueg<n_geno; trueg++)
-            result(trueg,trueg) = 1.0;
-        // male X
-        for(int trueg=0; trueg<n_alleles; trueg++)
-            result(trueg+n_geno, trueg) = 1.0;
-
-        return result;
-    }
-    else { // autosome
-        NumericMatrix result(n_geno,n_alleles);
+    NumericMatrix result(n_geno,n_geno);
 
-        for(int trueg=0; trueg<n_geno; trueg++)
-            result(trueg,trueg) = 1.0;
+    for(int trueg=0; trueg<n_geno; trueg++)
+        result(trueg,trueg) = 1.0;
 
-        return result;
-    }
+    return result;
 }
 
 // check that sex conforms to expectation
@@ -332,24 +303,12 @@ const std::vector<std::string> DOF1::geno_names(const std::vector<std::string> a
 {
     int n_alleles = alleles.size();
 
-    if(is_x_chr) {
-        std::vector<std::string> result(n_alleles*2);
+    std::vector<std::string> result(n_alleles);
 
-        for(int i=0; i<n_alleles; i++) {
-            result[i] = alleles[i] + "X";
-            result[i+n_alleles] = alleles[i] + "Y";
-        }
+    for(int i=0; i<n_alleles; i++)
+        result[i] = alleles[i];
 
-        return result;
-    }
-    else {
-        std::vector<std::string> result(n_alleles);
-
-        for(int i=0; i<n_alleles; i++)
-            result[i] = alleles[i];
-
-        return result;
-    }
+    return result;
 }
 
 const double DOF1::est_rec_frac(const NumericVector& gamma, const bool is_x_chr,

src/cross_hsf1.cpp

@@ -23,12 +23,7 @@ const bool HSF1::check_geno(const int gen, const bool is_observed_value,
     const int n_alleles = 8;
     const int n_geno = 8;
 
-    if(!is_x_chr || is_female) { // autosome or female X
-        if(gen>= 1 && gen <= n_geno) return true;
-    }
-    else { // male X
-        if(gen>=n_geno+1 && gen <=n_geno+n_alleles) return true;
-    }
+    if(gen>= 1 && gen <= n_geno) return true;
 
     return false; // otherwise a problem
 }
@@ -56,13 +51,15 @@ const double HSF1::emit(const int obs_gen, const int true_gen, const double erro
 
     if(obs_gen==0) return 0.0; // missing
 
-    int f1;
-    if(!is_x_chr || is_female) // autosome or female X
-        f1 = founder_geno[true_gen-1];
-    else
-        f1 = founder_geno[true_gen-9];
+    int f1 = founder_geno[true_gen-1];
 
-    int f2 = founder_geno[8]; // 9th founder is the other strain
+    int f2;
+    if(is_x_chr && !is_female) {
+        f2 = f1; // assuming female DO x male 9th strain, so male is hemizygous DO chr
+    } else {
+        // autosome or female X chr
+        f2 = founder_geno[8]; // 9th founder is the other strain
+    }
 
     // treat founder hets as missing
     if(f1==2) f1 = 0;
@@ -160,30 +157,17 @@ const double HSF1::step(const int gen_left, const int gen_right, const double re
 const IntegerVector HSF1::possible_gen(const bool is_x_chr, const bool is_female,
                                        const IntegerVector& cross_info)
 {
-    int n_alleles = 8;
     int n_geno = 8;
 
-    if(is_x_chr && !is_female) { // male X chromosome
-        IntegerVector result(n_alleles);
-        for(int i=0; i<n_alleles; i++)
-            result[i] = n_geno+i+1;
-        return result;
-    }
-    else { // autosome or female X
-        IntegerVector result(n_geno);
-        for(int i=0; i<n_geno; i++)
-            result[i] = i+1;
-        return result;
-    }
+    IntegerVector result(n_geno);
+    for(int i=0; i<n_geno; i++)
+        result[i] = i+1;
+    return result;
 }
 
 const int HSF1::ngen(const bool is_x_chr)
 {
-    int n_alleles = 8;
-    int n_geno = 8;
-
-    if(is_x_chr) return n_geno+n_alleles;
-    return n_geno;
+    return 8;
 }
 
 const int HSF1::nalleles()
@@ -193,28 +177,14 @@ const int HSF1::nalleles()
 
 const NumericMatrix HSF1::geno2allele_matrix(const bool is_x_chr)
 {
-    const int n_alleles = 8;
     const int n_geno = 8;
 
-    if(is_x_chr) {
-        NumericMatrix result(n_geno+n_alleles, n_alleles);
-        // female X
-        for(int trueg=0; trueg<n_geno; trueg++)
-            result(trueg,trueg) = 1.0;
-        // male X
-        for(int trueg=0; trueg<n_alleles; trueg++)
-            result(trueg+n_geno, trueg) = 1.0;
+    NumericMatrix result(n_geno,n_geno);
 
-        return result;
-    }
-    else { // autosome
-        NumericMatrix result(n_geno,n_alleles);
-
-        for(int trueg=0; trueg<n_geno; trueg++)
-            result(trueg,trueg) = 1.0;
+    for(int trueg=0; trueg<n_geno; trueg++)
+        result(trueg,trueg) = 1.0;
 
-        return result;
-    }
+    return result;
 }
 
 // check that sex conforms to expectation
@@ -330,24 +300,12 @@ const std::vector<std::string> HSF1::geno_names(const std::vector<std::string> a
 {
     int n_alleles = alleles.size();
 
-    if(is_x_chr) {
-        std::vector<std::string> result(n_alleles*2);
-
-        for(int i=0; i<n_alleles; i++) {
-            result[i] = alleles[i] + "X";
-            result[i+n_alleles] = alleles[i] + "Y";
-        }
-
-        return result;
-    }
-    else {
-        std::vector<std::string> result(n_alleles);
+    std::vector<std::string> result(n_alleles);
 
-        for(int i=0; i<n_alleles; i++)
-            result[i] = alleles[i];
+    for(int i=0; i<n_alleles; i++)
+        result[i] = alleles[i];
 
-        return result;
-    }
+    return result;
 }
 
 const double HSF1::est_rec_frac(const NumericVector& gamma, const bool is_x_chr,