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cape  

Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice
View on CRAN: Click here


Download and install cape package within the R console
Install from CRAN:
install.packages("cape")

Install from Github:
library("remotes")
install_github("cran/cape")

Install by package version:
library("remotes")
install_version("cape", "3.1.2")



Attach the package and use:
library("cape")
Maintained by
Anna Tyler
[Scholar Profile | Author Map]
First Published: 2013-04-04
Latest Update: 2022-05-19
Description:
Combined Analysis of Pleiotropy and Epistasis infers predictive networks between genetic variants and phenotypes. It can be used with standard two-parent populations as well as multi-parent populations, such as the Diversity Outbred (DO) mice, Collaborative Cross (CC) mice, or the multi-parent advanced generation intercross (MAGIC) population of Arabidopsis thaliana. It uses complementary information of pleiotropic gene variants across different phenotypes to resolve models of epistatic interactions between alleles. To do this, cape reparametrizes main effect and interaction coefficients from pairwise variant regressions into directed influence parameters. These parameters describe how alleles influence each other, in terms of suppression and enhancement, as well as how gene variants influence phenotypes. All of the final interactions are reported as directed interactions between pairs of parental alleles. For detailed descriptions of the methods used in this package please see the following references. Carter, G. W., Hays, M., Sherman, A. & Galitski, T. (2012) . Tyler, A. L., Lu, W., Hendrick, J. J., Philip, V. M. & Carter, G. W. (2013) .
How to cite:
Anna Tyler (2013). cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice. R package version 3.1.2, https://cran.r-project.org/web/packages/cape. Accessed 09 May. 2025.
Previous versions and publish date:
1.0 (2013-04-04 16:52), 1.1 (2013-06-05 21:53), 1.2 (2013-08-03 18:43), 1.3 (2014-09-26 18:50), 2.0.1 (2016-04-06 18:11), 2.0.2 (2016-06-09 19:59), 2.0 (2016-03-29 18:59), 3.1.0 (2021-02-10 12:30), 3.1.1 (2022-05-19 15:40)
Other packages that cited cape R package
View cape citation profile
Other R packages that cape depends, imports, suggests or enhances
Complete documentation for cape
Functions, R codes and Examples using the cape R package
Some associated functions: Cape-class . bin_curve . bin_vector . calc_delta_errors . calc_emp_p . calc_m . calc_p . cape2mpp . center_std . check_bad_markers . check_communities . check_geno . check_underscore . chunkV . colors_from_values . compare_markers . consec_pairs . delete_underscore . direct_influence . draw_pie . error_prop . exp_color_fun . flatten_array . genome_wide_threshold_1D . get_allele_colors . get_block_allele . get_circle . get_col_num . get_color . get_color2 . get_concent_circ . get_covar . get_eigentraits . get_geno . get_geno_dim . get_geno_with_covar . get_interaction_error . get_layout_mat . get_line . get_linearly_independent . get_marker_chr . get_marker_covar . get_marker_idx . get_marker_location . get_marker_name . get_marker_num . get_network . get_pairs_for_pairscan . get_pheno . get_stats_multiallele . hist_pheno . image_with_text . impute_missing_geno . kin_adjust . kinship . linkage_blocks_network . load_input_and_run_cape . marker2covar . my_image_plot . norm_pheno . one_pairscan_parallel . one_singlescanDO . pair_matrix . pairscan . pairscan_kin . pairscan_noKin . pairscan_null . pairscan_null_kin . pheatmap_generate_breaks . pheatmap_scale_colours . pheno2covar . plink2cape . plot_bars . plot_effects . plot_full_network . plot_int_heat . plot_lines . plot_network . plot_pairscan . plot_pheno_cor . plot_points . plot_singlescan . plot_svd . plot_trait_circ . plot_variant_influences . qnorm_pheno . qtl2_to_cape . read_parameters . read_population . remove_ind . remove_kin_ind . remove_markers . remove_missing_genotype_data . remove_unused_markers . report_progress . rotate_mat . run_cape . rz_transform . segment_region . select_eigentraits . select_markers_for_pairscan . select_pheno . singlescan . sort_by_then_by . write_population . write_variant_influences . 
Some associated R codes: Cape.R . bin_curve.R . bin_vector.R . calc_delta_errors.R . calc_emp_p.R . calc_m.R . calc_p.R . cape2mpp.R . center_std.R . check_bad_markers.R . check_communities.R . check_geno.R . check_underscore.R . chunkV.R . colors_from_values.R . compare_markers.R . consec_pairs.R . delete_underscore.R . direct_influence.R . draw_pie.R . error_prop.R . exp_color_fun.R . flatten_array.R . genome_wide_threshold_1D.R . get_allele_colors.R . get_block_allele.R . get_circle.R . get_col_num.R . get_color.R . get_color2.R . get_concent_circ.R . get_covar.R . get_eigentraits.R . get_geno.R . get_geno_dim.R . get_geno_with_covar.R . get_interaction_error.R . get_layout_mat.R . get_line.R . get_linearly_independent.R . get_marker_chr.R . get_marker_covar.R . get_marker_idx.R . get_marker_location.R . get_marker_name.R . get_marker_num.R . get_network.R . get_pairs_for_pairscan.R . get_pheno.R . get_stats_multiallele.R . hist_pheno.R . image_with_text.R . impute_missing_geno.R . kin_adjust.R . kinship.R . linkage_blocks_network.R . load_input_and_run_cape.R . marker2covar.R . my_image_plot.R . norm_pheno.R . one_pairscan_parallel.R . one_singlescanDO.R . pair_matrix.R . pairscan.R . pairscan_kin.R . pairscan_noKin.R . pairscan_null.R . pairscan_null_kin.R . pheatmap_generate_breaks.R . pheatmap_scale_colours.R . pheno2covar.R . plink2cape.R . plot_bars.R . plot_effects.R . plot_full_network.R . plot_int_heat.R . plot_lines.R . plot_network.R . plot_pairscan.R . plot_pheno_cor.R . plot_points.R . plot_singlescan.R . plot_svd.R . plot_trait_circ.R . plot_variant_influences.R . qnorm_pheno.R . qtl2_to_cape.R . read_parameters.R . read_population.R . remove_ind.R . remove_kin_ind.R . remove_markers.R . remove_missing_genotype_data.R . remove_unused_markers.R . report_progress.R . rotate_mat.R . run_cape.R . rz_transform.R . segment_region.R . select_eigentraits.R . select_markers_for_pairscan.R . select_pheno.R . singlescan.R . sort_by_then_by.R . write_population.R . write_variant_influences.R .  Full cape package functions and examples
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