Man pages for TheJacksonLaboratory/cape
Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice
| bin_curve | Bins a single scan curve into peaks automatically |
| bin_vector | Snap continuous values to a grid |
| calc_delta_errors | Error propagation |
| calc_emp_p | Calculate empirical p-values |
| calc_m | Calculate m |
| calc_p | Calculate P Values for Interactions Based on Permutations |
| cape2mpp | Converts a 'read_population' object to a multi-parent object |
| Cape-class | The CAPE data object |
| center_std | This function mean centers and standardizes a vector |
| check_bad_markers | Checks for unused markers |
| check_communities | Check community assignments |
| check_geno | Check to see if the any markers in the supplied genotype... |
| check_underscore | Checks for underscores in marker names |
| chunkV | Bins a vector into chunks |
| colors_from_values | Retrieve colors based on numeric values |
| compare_markers | Removes markers from data_obj that are not present in the... |
| consec_pairs | Generate a matrix of consecutive elements |
| delete_underscore | Delete underscores from marker names |
| direct_influence | Calculate the significance of direct influences of variant... |
| draw_pie | Draw a pie chart |
| error_prop | Estimate Errors of Regression Coefficients |
| exp_color_fun | Exponential color function |
| flatten_array | Drop the 3rd dimension of an array using a summary function,... |
| genome_wide_threshold_1D | Calculate a genome-wide significance threshold for the... |
| get_allele_colors | Get DO colors |
| get_block_allele | Get allele assignments for linkage blocks |
| get_circle | Generate coordinates for a circle |
| get_col_num | Find column numbers using column names |
| get_color | get a hex color string |
| get_color2 | Generate color ramp |
| get_concent_circ | Generate list of concentric circles |
| get_covar | Get covariate information |
| get_eigentraits | Calculate eigentraits |
| get_geno | Gets the geno object |
| get_geno_dim | Returns which dimensions the individual, locus, and alleles... |
| get_geno_with_covar | Return the genotype matrix with covariates added. |
| get_interaction_error | Get error bars for interaction plot |
| get_layout_mat | Get the best layout matrix for a given number of panes per... |
| get_line | Get line coordinates |
| get_linearly_independent | Check selected markers for linear independence. |
| get_marker_chr | Get chromosome numbers for markers |
| get_marker_covar | Get genotype or covariate values |
| get_marker_idx | Get original indices for markers |
| get_marker_location | Get marker genomic position |
| get_marker_name | Get marker names |
| get_marker_num | Get numbers for markers |
| get_network | Convert the final results to an adjacency matrix. |
| get_pairs_for_pairscan | Select marker pairs for pairscan |
| get_pheno | Get the phenotype matrix |
| get_stats_multiallele | Perform linear regression on multi-allele markers. |
| hist_pheno | Plot trait histograms |
| image_with_text | Plot a heatmap |
| impute_missing_geno | Impute missing genotype data using k nearest neighbors |
| kin_adjust | Corrects genotypes, phenotypes, and covariates for kinship. |
| kinship | Calculate the kinship matrix |
| linkage_blocks_network | Identify linkage blocks |
| load_input_and_run_cape | Loads input and run CAPE |
| marker2covar | Creates a covariate from a genetic marker |
| my_image_plot | Generate a Heatmap-type image |
| norm_pheno | Mean-center and normalize phenotypes |
| one_pairscan_parallel | This is an internal function to run a single pairscan It is... |
| one_singlescanDO | Performs marker regression |
| pair_matrix | Get all pairs of elements in a vector |
| pairscan | This function performs the pairwise scan on all markers. |
| pairscan_kin | Run the pairscan with a kinship correction |
| pairscan_noKin | Perform pairscan without a kinship correction |
| pairscan_null | Generate a null distribution for the pairscan. |
| pairscan_null_kin | Generates a null distribution for the pairscan |
| pheatmap_generate_breaks | pheatmap generate breaks found at this link... |
| pheatmap_scale_colours | pheatmap scale colours found at this link... |
| pheno2covar | Create a covariate from a trait |
| plink2cape | Convert plink2 files to cape format |
| plot_bars | Plot phenotypic effect for two markers as a bar plot |
| plot_effects | Plot Interaction Effects |
| plot_full_network | Plot the final epistatic network in a traditional network... |
| plot_int_heat | Plot phenotypic effects for two markers as a heat map |
| plot_lines | Plot interaction plot for traits and genetic markers |
| plot_network | Plots cape results as a circular network |
| plot_pairscan | Plot the result of the pairwise scan |
| plot_pheno_cor | Plot trait pairs against each other |
| plot_points | Plot phenotypic effect for two markers as points |
| plot_singlescan | Plot results of single-locus scans |
| plot_svd | Plots eigentraits |
| plot_trait_circ | Plot concentric trait circles |
| plot_variant_influences | Plot cape coefficients |
| qnorm_pheno | Plot trait distributions |
| qtl2_to_cape | Convert qtl2 object to cape format |
| read_parameters | Read the parameter file, add missing entries |
| read_population | Reads in data in the R/qtl csv format |
| remove_ind | Remove individuals |
| remove_kin_ind | Removes individuals from the kinship object to match the... |
| remove_markers | Removes genetic markers |
| remove_missing_genotype_data | Removes individuals and/or markers with missing data |
| remove_unused_markers | Take out markers not used in cape |
| report_progress | Report Progress of a Process |
| rotate_mat | Orients a matrix for proper display in a plot |
| run_cape | Runs CAPE |
| rz_transform | Rank Z normalize |
| segment_region | Divide a region into equal parts. |
| select_eigentraits | Assign selected eigentraits in the Cape object |
| select_markers_for_pairscan | Select markers for the pairwise scan. |
| select_pheno | This function selects the phenotypes in a Cape object |
| singlescan | Runs marker regression on each individual genetic marker |
| sort_by_then_by | Sort a table by a list of columns |
| write_population | Save the cross data in R/qtl CSV format |
| write_variant_influences | Write significant cape interactions to a csv file |
