running tests + with chr2 of apple and still seeing discrepancy which…

… is not attributed to genome-wide LD calculation but most likely to distance estimation difference between binary data and continuous allele frequency data
jeffersonfparil · Dec 31, 2023 · 97a3ac8 · 97a3ac8
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diff --git a/README.md b/README.md
@@ -181,6 +181,7 @@ This is used for genotype classes, i.e., binned allele frequencies: $g = {{1 \ov
 ### Diploid (Apple) mean absolute error
 
 ![mae_barplots](./res/apple-Mean_absolute_error.svg)
+![mae_barplots](./res/applechr_2-Mean_absolute_error.svg)
 
 ### Diploid (Grape) mean absolute error
 
@@ -205,6 +206,7 @@ This is used for genotype classes, i.e., binned allele frequencies: $g = {{1 \ov
 ### Diploid (Apple) concordance of observed and imputed genotype classes
 
 ![concordance_genotype_classes_barplots](./res/apple-Concordance.svg)
+![concordance_genotype_classes_barplots](./res/applechr_2-Concordance.svg)
 
 ### Diploid (Grape) concordance of observed and imputed genotype classes
 
@@ -229,6 +231,7 @@ This is used for genotype classes, i.e., binned allele frequencies: $g = {{1 \ov
 ### Diploid (Apple) coefficient of determination
 
 ![r2_barplots](./res/apple-Coefficient_of_determination.svg)
+![r2_barplots](./res/applechr_2-Coefficient_of_determination.svg)
 
 ### Diploid (Grape) coefficient of determination
 

diff --git a/res/grape-Coefficient_of_determination.svg b/res/grape-Coefficient_of_determination.svg
diff --git a/res/grape-Concordance.svg b/res/grape-Concordance.svg
diff --git a/res/grape-Mean_absolute_error.svg b/res/grape-Mean_absolute_error.svg
diff --git a/res/lucerne-Coefficient_of_determination.svg b/res/lucerne-Coefficient_of_determination.svg
diff --git a/res/lucerne-Concordance.svg b/res/lucerne-Concordance.svg
diff --git a/res/lucerne-Mean_absolute_error.svg b/res/lucerne-Mean_absolute_error.svg
diff --git a/res/perf.md b/res/perf.md
@@ -73,6 +73,12 @@ mv LinkImpute.data.grape.num.raw.txt.vcf grape.vcf
 # grep "^##Extracted" grape.vcf >> grapeS2.vcf
 # grep "^#CHROM" grape.vcf >> grapeS2.vcf
 # grep "^S2" grape.vcf >> grapeS2.vcf
+### (6) diploid apple single chromosome
+head -n1 apple.vcf > applechr_2.vcf
+grep "^##chr_2" apple.vcf >> applechr_2.vcf
+grep "^##Extracted" apple.vcf >> applechr_2.vcf
+grep "^#CHROM" apple.vcf >> applechr_2.vcf
+grep "^chr_2" apple.vcf >> applechr_2.vcf
 ```
 
 *ssv2vcf.R* - convert space-delimited genotype data from LinkImpute paper

diff --git a/res/perf.slurm b/res/perf.slurm
@@ -40,4 +40,4 @@ done
 rm ploidy_vcf-${SLURM_ARRAY_TASK_ID}.tmp
 
 ### Execute:
-# sbatch --array=1-24%12 perf.slurm
+# sbatch --array=1-44 perf.slurm