Files in JH-Zhou/HandyCNV
HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature-request.md
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
HandyCNV.Rproj
LICENSE.md
NAMESPACE
R/call_cnvr.R
R/call_gene.R
R/cnv_clean.R
R/cnv_summary.R
R/cnv_visualising.R
R/cnvr_plot.R
R/compare_cnv.R
R/compare_cnvr.R
R/compare_gene.R
R/convert_coord.R
R/convert_map_coord.R
R/generate_dome_data.R
R/get_haplotype.R
R/get_refgene.R
R/get_samples.R
R/globals.R
R/plot_cnvr_panorama.R
R/plot_cnvr_source.R
R/roh_visual.R
R/roh_window.R
R/snp_density_plot.R
README.md
_pkgdown.yml
codecov.yml
docs/404.html
docs/LICENSE.html
docs/_config.yml
docs/articles/Chr7_11_12.png
docs/articles/HandyCNV.html
docs/articles/HandyCNV_files/figure-html/unnamed-chunk-11-1.png
docs/articles/HandyCNV_files/figure-html/unnamed-chunk-22-1.png
docs/articles/HandyCNV_files/figure-html/unnamed-chunk-37-1.png
docs/articles/HandyCNV_files/figure-html/unnamed-chunk-38-1.png
docs/articles/HandyCNV_files/header-attrs-2.6/header-attrs.js
docs/articles/cnv_summary_plot_Penn/cnv_summaray_plot_2.png
docs/articles/cnv_summary_plot_Penn/cnv_summary_plot_1.png
docs/articles/cnv_visual/BLA-DQB.png
docs/articles/cnv_visual/CNV_of_201094560076_R03C02.png
docs/articles/cnv_visual/Chr15_77-80.1221Mb.png
docs/articles/cnv_visual/Chr23_25.56-25.74Mb.png
docs/articles/cnv_visual_all_part/Chr28.png
docs/articles/cnv_visual_all_penn/Chr15.png
docs/articles/cnvr_panorama_classical_ld/7_310937_435584_Mixed.png
docs/articles/cnvr_panorama_heat_ld/7_310937_435584_Mixed.png
docs/articles/cnvr_plot_part/cnvr_plot.png
docs/articles/cnvr_plot_penn/cnvr_plot.png
docs/articles/compare_cnv_PartUMD_Vs_PennUMD/combine.png
docs/articles/compare_cnvr_PartUMD_Penn_UMD/combine_cnvr.png
docs/articles/compare_gene_Part_Vs_Penn/two_lists_comparison.png
docs/articles/compare_gene_four_lists/four_gene_heatmap.png
docs/articles/compare_gene_three_lists/threegene.png
docs/articles/convert_map/SNP_difference_density.png
docs/articles/convert_map/comparison_snp.png
docs/articles/high_freq_cnvr_penn/combine_cnvr.png
docs/articles/index.html
docs/articles/plot_cnvr_source/Chr14_50.591566-54.441985Mb_Source.png
docs/articles/roh_visual/Chr11_roh.png
docs/articles/roh_visual/Chr6_36.5-40.5Mb_roh.png
docs/articles/roh_visual/Chr6_36.5-40.61Mb_roh.png
docs/articles/roh_visual/Chr6_36.5-40.6Mb_roh.png
docs/articles/roh_visual/Chr6_38.25_39.52_roh.png
docs/articles/roh_visual/ROH_of_201094560008_R04C01.png
docs/articles/roh_window/roh_freq_windows.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/call_cnvr.html
docs/reference/call_gene.html
docs/reference/clean_ensgene.html
docs/reference/clean_ucsc.html
docs/reference/closer_snp.html
docs/reference/cnv_clean.html
docs/reference/cnv_summary_plot.html
docs/reference/cnv_visual.html
docs/reference/cnvr_plot.html
docs/reference/compare_cnv.html
docs/reference/compare_cnvr.html
docs/reference/compare_gene.html
docs/reference/compare_interval.html
docs/reference/convert_coord.html
docs/reference/convert_map.html
docs/reference/get_demo.html
docs/reference/get_haplotype.html
docs/reference/get_refgene.html
docs/reference/index.html
docs/reference/plot_cnvr_panorama.html
docs/reference/plot_cnvr_source.html
docs/reference/plot_gene.html
docs/reference/prep_phased.html
docs/reference/roh_visual.html
docs/reference/roh_window.html
inst/extdata/Demo_data/Pedigree/Pedigree.csv
inst/extdata/Demo_data/Readme.txt
inst/extdata/Demo_data/cnv_results/ARS_PennCNV_WGC.goodcnv
inst/extdata/Demo_data/cnv_results/UMD_CNVPartition.txt
inst/extdata/Demo_data/cnv_results/UMD_Standard_CNV.txt
inst/extdata/Demo_data/demo_intensity.txt
inst/extdata/Demo_data/map/ARS1.2_GGPHDV3.map
inst/extdata/Demo_data/map/UMD3.1_Bovine.map
inst/extdata/Demo_data/umd_Plink_penncnv/demo_HandyCNV.bed
inst/extdata/Demo_data/umd_Plink_penncnv/demo_HandyCNV.bim
inst/extdata/Demo_data/umd_Plink_penncnv/demo_HandyCNV.fam
man/call_cnvr.Rd
man/call_gene.Rd
man/clean_ensgene.Rd
man/clean_ucsc.Rd
man/closer_snp.Rd
man/cnv_clean.Rd
man/cnv_summary_plot.Rd
man/cnv_visual.Rd
man/cnvr_plot.Rd
man/compare_cnv.Rd
man/compare_cnvr.Rd
man/compare_gene.Rd
man/compare_interval.Rd
man/convert_coord.Rd
man/convert_map.Rd
man/figures/High_resolution_pipeline_HandyCNV.jpg
man/get_demo.Rd
man/get_haplotype.Rd
man/get_refgene.Rd
man/get_samples.Rd
man/haplo_visual.Rd
man/plot_cnvr_panorama.Rd
man/plot_cnvr_source.Rd
man/plot_gene.Rd
man/plot_snp_density.Rd
man/prep_phased.Rd
man/roh_visual.Rd
man/roh_window.Rd
vignettes/.gitignore
vignettes/BMP7.jpg
vignettes/Chr7_11_12.png
vignettes/Demo_data/demo.map
vignettes/Demo_data/demo.ped
vignettes/Demo_data/demo_HandyCNV.bed
vignettes/Demo_data/demo_HandyCNV.bim
vignettes/Demo_data/demo_HandyCNV.fam
vignettes/Demo_data/demo_intensity.txt
vignettes/HandyCNV.Rmd
vignettes/UMD_Vs_ARS_CNV/checkover_indiv_1.png
vignettes/UMD_Vs_ARS_CNV/checkover_indiv_1.summary
vignettes/UMD_Vs_ARS_CNV/checkover_indiv_2.png
vignettes/UMD_Vs_ARS_CNV/checkover_indiv_2.summary
vignettes/UMD_Vs_ARS_CNV/checkover_pop_1.png
vignettes/UMD_Vs_ARS_CNV/checkover_pop_1.summary
vignettes/UMD_Vs_ARS_CNV/checkover_pop_2.png
vignettes/UMD_Vs_ARS_CNV/checkover_pop_2.summary
vignettes/UMD_Vs_ARS_CNV/checkover_pop_2.txt
vignettes/UMD_Vs_ARS_CNV/cleancnv_AtoU.coord
vignettes/UMD_Vs_ARS_CNV/cleancnv_UtoA.coord
vignettes/UMD_Vs_ARS_CNV/cnv_all_indiv_2.checkoverlap
vignettes/UMD_Vs_ARS_CNV/cnv_all_population_1.checkoverlap
vignettes/UMD_Vs_ARS_CNV/non_overlap_cnv.indiv
vignettes/UMD_Vs_ARS_CNV/non_overlap_cnv.popu
vignettes/UMD_Vs_ARS_CNV/non_overlap_cnv_ars.indiv
vignettes/UMD_Vs_ARS_CNV/non_overlap_cnv_ars.popu
vignettes/UMD_Vs_ARS_CNV/overlap_cnv.indiv
vignettes/UMD_Vs_ARS_CNV/overlap_cnv.popu
vignettes/UMD_Vs_ARS_CNV/overlap_cnv.summary
vignettes/UMD_Vs_ARS_CNV/overlap_cnv_2.summary
vignettes/UMD_Vs_ARS_CNV/overlap_cnv_ars.indiv
vignettes/UMD_Vs_ARS_CNV/overlap_cnv_ars.popu
vignettes/call_cnvr_Part/cnvr.txt
vignettes/call_cnvr_Part/cnvr_chr_summary.txt
vignettes/call_cnvr_Part/cnvr_summary.txt
vignettes/call_cnvr_Part/individual_cnv_cnvr.txt
vignettes/call_cnvr_Part/no_freq_cnvr.txt
vignettes/call_cnvr_Penn/cnvr.txt
vignettes/call_cnvr_Penn/cnvr_chr_summary.txt
vignettes/call_cnvr_Penn/cnvr_summary.txt
vignettes/call_cnvr_Penn/individual_cnv_cnvr.txt
vignettes/call_cnvr_Penn/no_freq_cnvr.txt
vignettes/call_cnvr_part/cnvr.txt
vignettes/call_cnvr_part/cnvr_chr_summary.txt
vignettes/call_cnvr_part/cnvr_summary.txt
vignettes/call_cnvr_part/individual_cnv_cnvr.txt
vignettes/call_cnvr_part/no_freq_cnvr.txt
vignettes/call_cnvr_penn/cnvr.txt
vignettes/call_cnvr_penn/cnvr_chr_summary.txt
vignettes/call_cnvr_penn/cnvr_summary.txt
vignettes/call_cnvr_penn/individual_cnv_cnvr.txt
vignettes/call_cnvr_penn/no_freq_cnvr.txt
vignettes/call_cnvr_standard/cnvr.txt
vignettes/call_cnvr_standard/cnvr_chr_summary.txt
vignettes/call_cnvr_standard/cnvr_summary.txt
vignettes/call_cnvr_standard/individual_cnv_cnvr.txt
vignettes/call_cnvr_standard/no_freq_cnvr.txt
vignettes/call_gene_Part/call_gene_summary.txt
vignettes/call_gene_Part/cnv_annotation.txt
vignettes/call_gene_Part/gene_freq_cnv.txt
vignettes/call_gene_Part/gene_list.annotation
vignettes/call_gene_Part/interval_annotation.txt
vignettes/call_gene_Part/interval_gene_summarise_table.txt
vignettes/call_gene_Penn_Ens/call_gene_summary.txt
vignettes/call_gene_Penn_Ens/cnv_annotation.txt
vignettes/call_gene_Penn_Ens/gene_freq_cnv.txt
vignettes/call_gene_Penn_Ens/gene_list.annotation
vignettes/call_gene_Penn_Ens/interval_annotation.txt
vignettes/call_gene_Penn_Ens/interval_gene_summarise_table.txt
vignettes/call_gene_Penn_UCSC/call_gene_summary.txt
vignettes/call_gene_Penn_UCSC/cnv_annotation.txt
vignettes/call_gene_Penn_UCSC/gene_freq_cnv.txt
vignettes/call_gene_Penn_UCSC/gene_list.annotation
vignettes/call_gene_Penn_UCSC/interval_annotation.txt
vignettes/call_gene_Penn_UCSC/interval_gene_summarise_table.txt
vignettes/call_gene_standard_ARS_UCSC/call_gene_summary.txt
vignettes/call_gene_standard_ARS_UCSC/cnv_annotation.txt
vignettes/call_gene_standard_ARS_UCSC/gene_freq_cnv.txt
vignettes/call_gene_standard_ARS_UCSC/gene_list.annotation
vignettes/call_gene_standard_ARS_UCSC/interval_annotation.txt
vignettes/call_gene_standard_ARS_UCSC/interval_gene_summarise_table.txt
vignettes/cnv_clean/cleancnv.cnv
vignettes/cnv_clean/cnv_summary.txt
vignettes/cnv_clean/cnvpart_clean.cnv
vignettes/cnv_clean/cnvpart_roh.cnv
vignettes/cnv_clean/cnvpart_summary.txt
vignettes/cnv_clean/penncnv_clean.cnv
vignettes/cnv_clean/penncnv_summary.txt
vignettes/cnv_summary_plot/cnv_summaray_plot_2.png
vignettes/cnv_summary_plot/cnv_summary_plot_1.png
vignettes/cnv_summary_plot/f1_cnv_distribution.png
vignettes/cnv_summary_plot/f2_length_group.png
vignettes/cnv_summary_plot/f3_lengthbox.png
vignettes/cnv_summary_plot/f4_chr.png
vignettes/cnv_summary_plot/f5_individual.png
vignettes/cnv_summary_plot/individual_cnv_count.txt
vignettes/cnv_summary_plot_Penn/cnv_distribution.png
vignettes/cnv_summary_plot_Penn/cnv_summaray_plot_2.png
vignettes/cnv_summary_plot_Penn/cnv_summary_plot_1.png
vignettes/cnv_summary_plot_Penn/f1_cnv_distribution.png
vignettes/cnv_summary_plot_Penn/f1a_lengthgroup.png
vignettes/cnv_summary_plot_Penn/f1b_lengthbox.png
vignettes/cnv_summary_plot_Penn/f1c_chr.png
vignettes/cnv_summary_plot_Penn/f1d_indiv.png
vignettes/cnv_summary_plot_Penn/f2_length_group.png
vignettes/cnv_summary_plot_Penn/f3_lengthbox.png
vignettes/cnv_summary_plot_Penn/f4_chr.png
vignettes/cnv_summary_plot_Penn/f5_individual.png
vignettes/cnv_summary_plot_Penn/individual_cnv_count.txt
vignettes/cnv_summary_plot_penn/cnv_summaray_plot_2.png
vignettes/cnv_summary_plot_penn/cnv_summary_plot_1.png
vignettes/cnv_summary_plot_penn/f1_cnv_distribution.png
vignettes/cnv_summary_plot_penn/f2_length_group.png
vignettes/cnv_summary_plot_penn/f3_lengthbox.png
vignettes/cnv_summary_plot_penn/f4_chr.png
vignettes/cnv_summary_plot_penn/f5_individual.png
vignettes/cnv_summary_plot_penn/individual_cnv_count.txt
vignettes/cnv_visual/BLA-DQB.png
vignettes/cnv_visual/CNV_of_201094560076_R03C02.png
vignettes/cnv_visual/Chr15_77-80.1221Mb.png
vignettes/cnv_visual/Chr23_25.56-25.74Mb.png
vignettes/cnv_visual_all_part/Chr1.png
vignettes/cnv_visual_all_part/Chr10.png
vignettes/cnv_visual_all_part/Chr11.png
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vignettes/cnv_visual_all_part/Chr14.png
vignettes/cnv_visual_all_part/Chr15.png
vignettes/cnv_visual_all_part/Chr16.png
vignettes/cnv_visual_all_part/Chr17.png
vignettes/cnv_visual_all_part/Chr18.png
vignettes/cnv_visual_all_part/Chr19.png
vignettes/cnv_visual_all_part/Chr2.png
vignettes/cnv_visual_all_part/Chr20.png
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vignettes/cnv_visual_all_part/Chr25.png
vignettes/cnv_visual_all_part/Chr26.png
vignettes/cnv_visual_all_part/Chr27.png
vignettes/cnv_visual_all_part/Chr28.png
vignettes/cnv_visual_all_part/Chr29.png
vignettes/cnv_visual_all_part/Chr3.png
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vignettes/cnv_visual_all_part/Chr8.png
vignettes/cnv_visual_all_part/Chr9.png
vignettes/cnv_visual_all_penn/Chr1.png
vignettes/cnv_visual_all_penn/Chr10.png
vignettes/cnv_visual_all_penn/Chr11.png
vignettes/cnv_visual_all_penn/Chr12.png
vignettes/cnv_visual_all_penn/Chr13.png
vignettes/cnv_visual_all_penn/Chr14.png
vignettes/cnv_visual_all_penn/Chr15.png
vignettes/cnv_visual_all_penn/Chr16.png
vignettes/cnv_visual_all_penn/Chr17.png
vignettes/cnv_visual_all_penn/Chr18.png
vignettes/cnv_visual_all_penn/Chr19.png
vignettes/cnv_visual_all_penn/Chr2.png
vignettes/cnv_visual_all_penn/Chr20.png
vignettes/cnv_visual_all_penn/Chr21.png
vignettes/cnv_visual_all_penn/Chr22.png
vignettes/cnv_visual_all_penn/Chr23.png
vignettes/cnv_visual_all_penn/Chr24.png
vignettes/cnv_visual_all_penn/Chr25.png
vignettes/cnv_visual_all_penn/Chr26.png
vignettes/cnv_visual_all_penn/Chr27.png
vignettes/cnv_visual_all_penn/Chr28.png
vignettes/cnv_visual_all_penn/Chr29.png
vignettes/cnv_visual_all_penn/Chr3.png
vignettes/cnv_visual_all_penn/Chr4.png
vignettes/cnv_visual_all_penn/Chr5.png
vignettes/cnv_visual_all_penn/Chr6.png
vignettes/cnv_visual_all_penn/Chr7.png
vignettes/cnv_visual_all_penn/Chr8.png
vignettes/cnv_visual_all_penn/Chr9.png
vignettes/cnvr_panorama_classical_ld/12_69804346_70777223_Mixed.png
vignettes/cnvr_panorama_classical_ld/15_78804694_79611716_Mixed.png
vignettes/cnvr_panorama_classical_ld/7_310937_435584_Mixed.png
vignettes/cnvr_panorama_heat_ld/12_56513728_64796304_Mixed.png
vignettes/cnvr_panorama_heat_ld/12_69804346_70777223_Mixed.png
vignettes/cnvr_panorama_heat_ld/15_78804694_79611716_Mixed.png
vignettes/cnvr_panorama_heat_ld/16_13872867_15634358_Mixed.png
vignettes/cnvr_panorama_heat_ld/20_43046657_49574742_Mixed.png
vignettes/cnvr_panorama_heat_ld/24_26177501_27839597_Mixed.png
vignettes/cnvr_panorama_heat_ld/7_310937_435584_Mixed.png
vignettes/cnvr_panorama_heat_ld/7_8782634_10494698_Mixed.png
vignettes/cnvr_plot.png
vignettes/cnvr_plot_part/cnvr_plot.png
vignettes/cnvr_plot_part/cnvr_plot.txt
vignettes/cnvr_plot_penn/cnvr_plot.png
vignettes/cnvr_plot_penn/cnvr_plot.txt
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_indiv_1.png
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_indiv_1.summary
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_indiv_2.png
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_indiv_2.summary
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_pop_1.png
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_pop_1.summary
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_pop_2.png
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_pop_2.summary
vignettes/compare_cnv_PartUMD_Vs_PennUMD/checkover_pop_2.txt
vignettes/compare_cnv_PartUMD_Vs_PennUMD/cnv_all_indiv_2.checkoverlap
vignettes/compare_cnv_PartUMD_Vs_PennUMD/cnv_all_inidv_1.checkoverlap
vignettes/compare_cnv_PartUMD_Vs_PennUMD/cnv_all_population_1.checkoverlap
vignettes/compare_cnv_PartUMD_Vs_PennUMD/combine.png
vignettes/compare_cnv_PartUMD_Vs_PennUMD/non_overlap_cnv_1.indiv
vignettes/compare_cnv_PartUMD_Vs_PennUMD/non_overlap_cnv_1.popu
vignettes/compare_cnv_PartUMD_Vs_PennUMD/non_overlap_cnv_tar.popu
vignettes/compare_cnv_PartUMD_Vs_PennUMD/non_overlap_cnv_tar_2.indiv
vignettes/compare_cnv_PartUMD_Vs_PennUMD/overlap_cnv_1.indiv
vignettes/compare_cnv_PartUMD_Vs_PennUMD/overlap_cnv_1.popu
vignettes/compare_cnv_PartUMD_Vs_PennUMD/overlap_cnv_1.summary
vignettes/compare_cnv_PartUMD_Vs_PennUMD/overlap_cnv_2.summary
vignettes/compare_cnv_PartUMD_Vs_PennUMD/overlap_cnv_tar.popu
vignettes/compare_cnv_PartUMD_Vs_PennUMD/overlap_cnv_tar_2.indiv
vignettes/compare_cnv_PartUMD_Vs_PennUMD/population_overlap_all.txt
vignettes/compare_cnvr/checkover_pop_1.png
vignettes/compare_cnvr/checkover_pop_1.summary
vignettes/compare_cnvr/checkover_pop_1.txt
vignettes/compare_cnvr/checkover_pop_2.txt
vignettes/compare_cnvr/non_overlap_cnv_1.popu
vignettes/compare_cnvr/non_overlap_cnv_ars.popu
vignettes/compare_cnvr/overlap_cnv_1.popu
vignettes/compare_cnvr/overlap_cnv_1.summary
vignettes/compare_cnvr/overlap_cnv_2.summary
vignettes/compare_cnvr/overlap_cnv_ars.popu
vignettes/compare_cnvr_PartUMD_Penn_UMD/checkover_pop_1.png
vignettes/compare_cnvr_PartUMD_Penn_UMD/checkover_pop_1.summary
vignettes/compare_cnvr_PartUMD_Penn_UMD/checkover_pop_1.txt
vignettes/compare_cnvr_PartUMD_Penn_UMD/checkover_pop_2.png
vignettes/compare_cnvr_PartUMD_Penn_UMD/checkover_pop_2.summary
vignettes/compare_cnvr_PartUMD_Penn_UMD/checkover_pop_2.txt
vignettes/compare_cnvr_PartUMD_Penn_UMD/combine_cnvr.png
vignettes/compare_cnvr_PartUMD_Penn_UMD/common_cnvr.txt
vignettes/compare_cnvr_PartUMD_Penn_UMD/non_overlap_cnvr_def.popu
vignettes/compare_cnvr_PartUMD_Penn_UMD/non_overlap_cnvr_tar.popu
vignettes/compare_cnvr_PartUMD_Penn_UMD/overlap_cnv_1.summary
vignettes/compare_cnvr_PartUMD_Penn_UMD/overlap_cnv_2.summary
vignettes/compare_cnvr_PartUMD_Penn_UMD/overlap_cnvr_def.popu
vignettes/compare_cnvr_PartUMD_Penn_UMD/overlap_cnvr_tar.popu
vignettes/compare_gene_Part_Vs_Penn/two_lists_comparison.png
vignettes/compare_gene_Part_Vs_Penn/two_lists_comparison.txt
vignettes/compare_gene_Part_Vs_Penn/two_lists_comparison_summary.txt
vignettes/compare_gene_four_lists/four_gene_comparison.txt
vignettes/compare_gene_four_lists/four_gene_comparison_summary.txt
vignettes/compare_gene_four_lists/four_gene_heatmap.png
vignettes/compare_gene_three_lists/three_genelists_comparison.txt
vignettes/compare_gene_three_lists/three_genelists_comparison_summary.txt
vignettes/compare_gene_three_lists/three_list_comparison.pdf
vignettes/compare_gene_three_lists/threegene.png
vignettes/compre_gene/four_gene_comparison.txt
vignettes/compre_gene/four_gene_comparison_summary.txt
vignettes/compre_gene/four_gene_heatmap.png
vignettes/convert_coord_penn_cnv/converted_coord.correct
vignettes/convert_coord_penn_cnv/converted_coord.txt
vignettes/convert_coord_penn_cnv/summary.txt
vignettes/convert_coord_penn_cnvR/cnvr_convert_coord.correct
vignettes/convert_coord_penn_cnvR/cnvr_convert_coord.txt
vignettes/convert_coord_penn_cnvR/converted_coord.correct
vignettes/convert_coord_penn_cnvR/converted_coord.txt
vignettes/convert_coord_penn_cnvR/summary.txt
vignettes/convert_map/SNP_difference_by_chromosome.png
vignettes/convert_map/SNP_difference_density.png
vignettes/convert_map/comparison_snp.png
vignettes/convert_map/def_tar_map.map
vignettes/convert_map/default_penncnv.map
vignettes/convert_map/diffirence_in_two_map.txt
vignettes/convert_map/snp_density_chromosome.txt
vignettes/convert_map/target_penncnv.map
vignettes/convert_map/target_plink.map
vignettes/high_freq_cnvr_penn/Chr12_56.513728-64.796304Mb.png
vignettes/high_freq_cnvr_penn/Chr12_69.804346-70.777223Mb.png
vignettes/high_freq_cnvr_penn/Chr15_78.804694-79.611716Mb.png
vignettes/high_freq_cnvr_penn/Chr16_13.872867-15.634358Mb.png
vignettes/high_freq_cnvr_penn/Chr20_43.046657-49.574742Mb.png
vignettes/high_freq_cnvr_penn/Chr24_26.177501-27.839597Mb.png
vignettes/high_freq_cnvr_penn/Chr7_0.310937-0.435584Mb.png
vignettes/high_freq_cnvr_penn/Chr7_8.782634-10.494698Mb.png
vignettes/high_freq_cnvr_penn/combine_cnvr.png
vignettes/orse_chr22_phased.vcf.gz
vignettes/overlap.txt
vignettes/plot_cnvr_source/Chr12_56.513728-64.796304Mb_Source.png
vignettes/plot_cnvr_source/Chr15_78.804694-79.611716Mb_Source.png
vignettes/refgene/Cow_ARS_ENS.txt
vignettes/refgene/Cow_ARS_UCSC.txt
vignettes/refgene/Cow_UMD_UCSC.txt
vignettes/refgene/cow_ARS_ENS.txt
vignettes/refgene/cow_ARS_UCSC.txt
vignettes/refgene/cow_UMD_UCSC.txt
vignettes/roh_visual/Chr11_roh.png
vignettes/roh_visual/Chr16_roh.png
vignettes/roh_visual/Chr6_35-42.5Mb_roh.png
vignettes/roh_visual/Chr6_36.5-40.5Mb_roh.png
vignettes/roh_visual/Chr6_36.5-40.61Mb_roh.png
vignettes/roh_visual/Chr6_36.5-40.6Mb_roh.png
vignettes/roh_visual/Chr6_38.25_39.52_roh.png
vignettes/roh_visual/Chr6_roh.png
vignettes/roh_visual/ROH_of_201094560008_R04C01.png
vignettes/roh_visual/ROH_of_201094560060_R02C01.png
vignettes/roh_window/high_freq_roh.txt
vignettes/roh_window/indiv_roh.txt
vignettes/roh_window/indiv_roh_inbreeding.txt
vignettes/roh_window/length_group_summary.txt
vignettes/roh_window/roh_freq.txt
vignettes/roh_window/roh_freq_windows.png
vignettes/snp_density.png
