Man pages for cape
Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

bin_curveBins a single scan curve into peaks automatically
bin_vectorSnap continuous values to a grid
calc_delta_errorsError propagation
calc_emp_pCalculate empirical p-values
calc_mCalculate m
calc_pCalculate P Values for Interactions Based on Permutations
cape2mppConverts a 'read_population' object to a multi-parent object
Cape-classThe CAPE data object
center_stdThis function mean centers and standardizes a vector
check_bad_markersChecks for unused markers
check_communitiesCheck community assignments
check_genoCheck to see if the any markers in the supplied genotype...
check_underscoreChecks for underscores in marker names
chunkVBins a vector into chunks
colors_from_valuesRetrieve colors based on numeric values
compare_markersRemoves markers from data_obj that are not present in the...
consec_pairsGenerate a matrix of consecutive elements
delete_underscoreDelete underscores from marker names
direct_influenceCalculate the significance of direct influences of variant...
draw_pieDraw a pie chart
error_propEstimate Errors of Regression Coefficients
exp_color_funExponential color function
flatten_arrayDrop the 3rd dimension of an array using a summary function,...
genome_wide_threshold_1DCalculate a genome-wide significance threshold for the...
get_allele_colorsGet DO colors
get_block_alleleGet allele assignments for linkage blocks
get_circleGenerate coordinates for a circle
get_col_numFind column numbers using column names
get_colorget a hex color string
get_color2Generate color ramp
get_concent_circGenerate list of concentric circles
get_covarGet covariate information
get_eigentraitsCalculate eigentraits
get_genoGets the geno object
get_geno_dimReturns which dimensions the individual, locus, and alleles...
get_geno_with_covarReturn the genotype matrix with covariates added.
get_interaction_errorGet error bars for interaction plot
get_layout_matGet the best layout matrix for a given number of panes per...
get_lineGet line coordinates
get_linearly_independentCheck selected markers for linear independence.
get_marker_chrGet chromosome numbers for markers
get_marker_covarGet genotype or covariate values
get_marker_idxGet original indices for markers
get_marker_locationGet marker genomic position
get_marker_nameGet marker names
get_marker_numGet numbers for markers
get_networkConvert the final results to an adjacency matrix.
get_pairs_for_pairscanSelect marker pairs for pairscan
get_phenoGet the phenotype matrix
get_stats_multiallelePerform linear regression on multi-allele markers.
hist_phenoPlot trait histograms
image_with_textPlot a heatmap
impute_missing_genoImpute missing genotype data using k nearest neighbors
kin_adjustCorrects genotypes, phenotypes, and covariates for kinship.
kinshipCalculate the kinship matrix
linkage_blocks_networkIdentify linkage blocks
load_input_and_run_capeLoads input and run CAPE
marker2covarCreates a covariate from a genetic marker
my_image_plotGenerate a Heatmap-type image
norm_phenoMean-center and normalize phenotypes
one_pairscan_parallelThis is an internal function to run a single pairscan It is...
one_singlescanDOPerforms marker regression
pair_matrixGet all pairs of elements in a vector
pairscanThis function performs the pairwise scan on all markers.
pairscan_kinRun the pairscan with a kinship correction
pairscan_noKinPerform pairscan without a kinship correction
pairscan_nullGenerate a null distribution for the pairscan.
pairscan_null_kinGenerates a null distribution for the pairscan
pheatmap_generate_breakspheatmap generate breaks found at this link...
pheatmap_scale_colourspheatmap scale colours found at this link...
pheno2covarCreate a covariate from a trait
plink2capeConvert plink2 files to cape format
plot_barsPlot phenotypic effect for two markers as a bar plot
plot_effectsPlot Interaction Effects
plot_full_networkPlot the final epistatic network in a traditional network...
plot_int_heatPlot phenotypic effects for two markers as a heat map
plot_linesPlot interaction plot for traits and genetic markers
plot_networkPlots cape results as a circular network
plot_pairscanPlot the result of the pairwise scan
plot_pheno_corPlot trait pairs against each other
plot_pointsPlot phenotypic effect for two markers as points
plot_singlescanPlot results of single-locus scans
plot_svdPlots eigentraits
plot_trait_circPlot concentric trait circles
plot_variant_influencesPlot cape coefficients
qnorm_phenoPlot trait distributions
qtl2_to_capeConvert qtl2 object to cape format
read_parametersRead the parameter file, add missing entries
read_populationReads in data in the R/qtl csv format
remove_indRemove individuals
remove_kin_indRemoves individuals from the kinship object to match the...
remove_markersRemoves genetic markers
remove_missing_genotype_dataRemoves individuals and/or markers with missing data
remove_unused_markersTake out markers not used in cape
report_progressReport Progress of a Process
rotate_matOrients a matrix for proper display in a plot
run_capeRuns CAPE
rz_transformRank Z normalize
segment_regionDivide a region into equal parts.
select_eigentraitsAssign selected eigentraits in the Cape object
select_markers_for_pairscanSelect markers for the pairwise scan.
select_phenoThis function selects the phenotypes in a Cape object
singlescanRuns marker regression on each individual genetic marker
sort_by_then_bySort a table by a list of columns
write_populationSave the cross data in R/qtl CSV format
write_variant_influencesWrite significant cape interactions to a csv file
cape documentation built on Feb. 10, 2021, 5:06 p.m.