R package citation, R package reverse dependencies, R package scholars, install an r package from GitHub hy is package acceptance pending why is package undeliverable amazon why is package on hold dhl tour packages why in r package r and r package full form why is r free why r is bad which r package to install which r package has which r package which r package version which r package readxl which r package ggplot which r package fread which r package license where is package.json where is package-lock.json where is package.swift where is package explorer in eclipse where is package where is package manager unity where is package installer android where is package manager console in visual studio who r package which r package to install which r package version who is package who is package deal who is package design r and r package full form r and r package meaning what r package has what package r what is package in java what is package what is package-lock.json what is package in python what is package.json what is package installer do r package can't install r packages r can't find package r can't load package can't load xlsx package r can't install psych package r can't install sf package r Write if else in NONMEM pk pd
cape
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]
[Scholar Profile | Author Map]
All associated links for this package
10.32614/CRAN.package.cape . cape results . cape.pdf . cape: A package for the combined analysis of pleiotropy and epistasis . cape_3.1.2.tar.gz . cape_3.1.2.zip . cape_3.1.2.zip . cape_3.1.2.zip . cape_3.1.2.tgz . cape_3.1.2.tgz . cape_3.1.2.tgz . cape_3.1.2.tgz . cape archive . https://CRAN.R-project.org/package=cape .
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:
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
nextGenShinyApps
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Obinna Obianom (view profile)
SACOBRA
Performs surrogate-assisted optimization for expensive black-box constrained problems. ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Samineh Bagheri (view profile)
disparityfilter
The disparity filter algorithm is a network reduction technique to
identify the 'backbone' structur ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Alessandro Bessi (view profile)
assertive.numbers
A set of predicates and assertions for checking the properties of
numbers. This is mainly for use ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Richard Cotton (view profile)
24,205
R Packages
207,311
Dependencies
65,402
Author Associations
24,206
Publication Badges
