Files in cape
Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/center_std.R
R/calc_m.R
R/linkage_blocks_network.R
R/plot_pheno_cor.R
R/get_marker_location.R
R/report_progress.R
R/read_parameters.R
R/write_variant_influences.R
R/write_population.R
R/bin_vector.R
R/sort_by_then_by.R
R/pheno2covar.R
R/get_pheno.R
R/Cape.R
R/get_line.R
R/get_geno_with_covar.R
R/get_marker_name.R
R/pairscan_null.R
R/remove_kin_ind.R
R/remove_ind.R
R/run_cape.R
R/load_input_and_run_cape.R
R/plot_network.R
R/flatten_array.R
R/get_marker_chr.R
R/pheatmap_generate_breaks.R
R/select_pheno.R
R/norm_pheno.R
R/image_with_text.R
R/read_population.R
R/rz_transform.R
R/error_prop.R
R/get_geno.R
R/pairscan_kin.R
R/chunkV.R
R/check_bad_markers.R
R/impute_missing_geno.R
R/hist_pheno.R
R/compare_markers.R
R/plink2cape.R
R/pheatmap_scale_colours.R
R/plot_lines.R
R/calc_delta_errors.R
R/plot_trait_circ.R
R/pairscan.R
R/select_markers_for_pairscan.R
R/get_geno_dim.R
R/select_eigentraits.R
R/get_covar.R
R/get_concent_circ.R
R/pairscan_noKin.R
R/kinship.R
R/get_allele_colors.R
R/get_circle.R
R/genome_wide_threshold_1D.R
R/draw_pie.R
R/get_marker_covar.R
R/get_color.R
R/singlescan.R
R/calc_p.R
R/kin_adjust.R
R/get_layout_mat.R
R/plot_points.R
R/consec_pairs.R
R/get_network.R
R/rotate_mat.R
R/get_interaction_error.R
R/plot_singlescan.R
R/plot_full_network.R
R/remove_missing_genotype_data.R
R/plot_bars.R
R/get_marker_idx.R
R/get_eigentraits.R
R/get_stats_multiallele.R
R/plot_variant_influences.R
R/pairscan_null_kin.R
R/get_color2.R
R/direct_influence.R
R/remove_markers.R
R/plot_svd.R
R/calc_emp_p.R
R/check_underscore.R
R/get_pairs_for_pairscan.R
R/one_pairscan_parallel.R
R/segment_region.R
R/get_linearly_independent.R
R/cape2mpp.R
R/pair_matrix.R
R/my_image_plot.R
R/get_block_allele.R
R/marker2covar.R
R/delete_underscore.R
R/bin_curve.R
R/check_geno.R
R/colors_from_values.R
R/one_singlescanDO.R
R/exp_color_fun.R
R/plot_pairscan.R
R/qtl2_to_cape.R
R/plot_int_heat.R
R/qnorm_pheno.R
R/remove_unused_markers.R
R/plot_effects.R
R/check_communities.R
R/get_col_num.R
R/get_marker_num.R
inst/doc/cape.R
inst/doc/cape.Rmd
inst/doc/cape.html
demo/demo_qtl2.R
demo/demo_rds.R
demo/demo_qtl.R
demo/00Index
demo/demo_plink.R
demo/demo_qtl/NON_NZO.parameters.yml
demo/demo_PLINK/plink.parameters.yml
demo/demo_rds/NON_NZO.parameters.yml
demo/demo_qtl2/iron.parameters.yml
build/vignette.rds
tests/testthat.R
tests/ci-tests.sh
tests/ci-tests.R
tests/testthat/test-cape-class.R
tests/testthat/test-run-cape.R
tests/testthat/helper.R
tests/testthat/test-load-input-and-run-cape.R
tests/testthat/test-get-pairscan-pairs.R
tests/testthat/testdata/demo_qtl_data/NON_NZO_Reifsnyder_pgm_CAPE_num.csv
tests/testthat/testdata/demo_qtl2_data/iron_covar.csv
tests/testthat/testdata/demo_qtl2_data/iron_pheno.csv
tests/testthat/testdata/demo_qtl2_data/iron_pmap.csv
tests/testthat/testdata/demo_qtl2_data/iron_gmap.csv
tests/testthat/testdata/demo_qtl2_data/iron_phenocovar.csv
tests/testthat/testdata/demo_qtl2_data/iron_geno.csv
tests/testthat/testdata/demo_qtl2_data/iron.yaml
tests/testthat/testdata/demo_PLINK_data/test.csv
tests/testthat/testdata/demo_PLINK_data/test.map
tests/testthat/testdata/demo_PLINK_data/test.pheno
tests/testthat/testdata/demo_PLINK_data/test.ped
tests/testthat/testdata/demo_rds_data/cape_geno.RDS
tests/testthat/testdata/demo_rds_data/cape_data.RDS
vignettes/Singlescan_ET1_Standardized.jpg
vignettes/Singlescan_ET2_Standardized.jpg
vignettes/reparam.png
vignettes/cape.md
vignettes/cape.Rmd
vignettes/cape.bib
man/get_col_num.Rd
man/pairscan_noKin.Rd
man/get_stats_multiallele.Rd
man/get_pheno.Rd
man/run_cape.Rd
man/remove_markers.Rd
man/get_marker_idx.Rd
man/plot_singlescan.Rd
man/get_layout_mat.Rd
man/kin_adjust.Rd
man/get_marker_num.Rd
man/remove_missing_genotype_data.Rd
man/pheno2covar.Rd
man/get_marker_name.Rd
man/get_geno_dim.Rd
man/plot_effects.Rd
man/linkage_blocks_network.Rd
man/get_line.Rd
man/cape2mpp.Rd
man/remove_kin_ind.Rd
man/report_progress.Rd
man/draw_pie.Rd
man/select_pheno.Rd
man/qtl2_to_cape.Rd
man/plot_pheno_cor.Rd
man/get_circle.Rd
man/calc_m.Rd
man/get_marker_location.Rd
man/plot_lines.Rd
man/kinship.Rd
man/exp_color_fun.Rd
man/plot_points.Rd
man/check_geno.Rd
man/get_pairs_for_pairscan.Rd
man/bin_vector.Rd
man/calc_delta_errors.Rd
man/plot_full_network.Rd
man/bin_curve.Rd
man/write_variant_influences.Rd
man/get_marker_chr.Rd
man/get_geno.Rd
man/get_color2.Rd
man/load_input_and_run_cape.Rd
man/norm_pheno.Rd
man/qnorm_pheno.Rd
man/rz_transform.Rd
man/get_block_allele.Rd
man/plot_bars.Rd
man/remove_ind.Rd
man/chunkV.Rd
man/delete_underscore.Rd
man/pheatmap_generate_breaks.Rd
man/get_color.Rd
man/read_parameters.Rd
man/singlescan.Rd
man/check_bad_markers.Rd
man/plot_svd.Rd
man/image_with_text.Rd
man/plot_int_heat.Rd
man/my_image_plot.Rd
man/plot_network.Rd
man/one_singlescanDO.Rd
man/calc_emp_p.Rd
man/plot_pairscan.Rd
man/direct_influence.Rd
man/get_interaction_error.Rd
man/get_geno_with_covar.Rd
man/get_covar.Rd
man/get_eigentraits.Rd
man/select_markers_for_pairscan.Rd
man/remove_unused_markers.Rd
man/consec_pairs.Rd
man/plot_trait_circ.Rd
man/pairscan_null.Rd
man/colors_from_values.Rd
man/plink2cape.Rd
man/write_population.Rd
man/hist_pheno.Rd
man/calc_p.Rd
man/sort_by_then_by.Rd
man/get_network.Rd
man/select_eigentraits.Rd
man/rotate_mat.Rd
man/get_allele_colors.Rd
man/pairscan_kin.Rd
man/segment_region.Rd
man/flatten_array.Rd
man/pairscan.Rd
man/get_marker_covar.Rd
man/read_population.Rd
man/pair_matrix.Rd
man/pairscan_null_kin.Rd
man/impute_missing_geno.Rd
man/center_std.Rd
man/plot_variant_influences.Rd
man/get_concent_circ.Rd
man/get_linearly_independent.Rd
man/check_communities.Rd
man/one_pairscan_parallel.Rd
man/Cape-class.Rd
man/compare_markers.Rd
man/marker2covar.Rd
man/pheatmap_scale_colours.Rd
man/check_underscore.Rd
man/genome_wide_threshold_1D.Rd
man/error_prop.Rd
