Files in cape

Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

NEWS.md README.md 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 demo/demo_qtl2.R demo/demo_rds.R demo/demo_qtl.R demo/demo_plink.R tests/testthat.R 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 vignettes/cape.Rmd 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