Other packages > Find by keyword >

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]
All associated links for this package
First Published: 2013-04-04
Latest Update:
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 07 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:24), 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), 3.1.2 (2024-01-09 12:00)
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

enrichwith  
Methods to Enrich R Objects with Extra Components
Provides the "enrich" method to enrich list-like R objects with new, relevant components. The curren ...
Download / Learn more Package Citations See dependency  
BayesESS  
Determining Effective Sample Size
Determines effective sample size of a parametric prior distribution in Bayesian models. For a web-b ...
Download / Learn more Package Citations See dependency  
modelwordcloud  
Model Word Clouds
Makes a word cloud of text, sized by the frequency of the word, and colored either by user-specified ...
Download / Learn more Package Citations See dependency  
bbricks  
Bayesian Methods and Graphical Model Structures for Statistical Modeling
A set of frequently used Bayesian parametric and nonparametric model structures, as well as a set of ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

28,083

R Packages

239,283

Dependencies

74,457

Author Associations

28,084

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA