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 09 Mar. 2026.
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), 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

rzentra  
Client for the 'ZENTRA Cloud' API
Provides functionality to read settings, statuses and readings of weather stations from the 'ZENTRA ...
Download / Learn more Package Citations See dependency  
ggblanket  
Simplify 'ggplot2' Visualisation
Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions. ...
Download / Learn more Package Citations See dependency  
pooling  
Fit Poolwise Regression Models
Functions for calculating power and fitting regression models in studies where a biomarker is measur ...
Download / Learn more Package Citations See dependency  
Rgb  
The R Genome Browser
Classes and methods to efficiently handle (slice, annotate, draw ...) genomic features (such as gene ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  

26,293

R Packages

225,784

Dependencies

70,376

Author Associations

26,294

Publication Badges

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