{ "_id": "6a275d4924555f66ed531b55", "Package": "qtl2", "Version": "0.41-10", "Date": "2026-06-08", "Title": "Quantitative Trait Locus Mapping in Experimental Crosses", "Description": "Provides a set of tools to perform quantitative trait\nlocus (QTL) analysis in experimental crosses. It is a\nreimplementation of the 'R/qtl' package to better handle\nhigh-dimensional data and complex cross designs. 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Cross colors", "object": "CCaltcolors", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "CCcolors", "title": "Collaborative Cross colors", "object": "CCcolors", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "CCorigcolors", "title": "Collaborative Cross colors", "object": "CCorigcolors", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "add_threshold", "title": "Add thresholds to genome scan plot", "topics": [ "add_threshold" ] }, { "page": "basic_summaries", "title": "Basic summaries of a cross2 object", "topics": [ "basic_summaries", "chr_names", "covar_names", "founders", "ind_ids", "ind_ids_covar", "ind_ids_geno", "ind_ids_gnp", "ind_ids_pheno", "marker_names", "n_chr", "n_covar", "n_founders", "n_ind", "n_ind_covar", "n_ind_geno", "n_ind_gnp", "n_ind_pheno", "n_mar", "n_pheno", "n_phenocovar", "phenocovar_names", "pheno_names", "tot_mar" ] }, { "page": "batch_cols", "title": "Batch columns by pattern of missing values", "topics": [ "batch_cols" ] }, { "page": "batch_vec", "title": "Split vector into batches", "topics": [ "batch_vec" ] }, { "page": "bayes_int", "title": "Calculate Bayes credible intervals", "topics": [ "bayes_int" ] }, { "page": "calc_entropy", "title": "Calculate entropy of genotype probability distribution", "topics": [ "calc_entropy" ] }, { "page": "calc_errorlod", "title": "Calculate genotyping error LOD scores", "topics": [ "calc_errorlod" ] }, { "page": "calc_geno_freq", "title": "Calculate genotype frequencies", "topics": [ "calc_geno_freq" ] }, { "page": "calc_genoprob", "title": "Calculate conditional genotype probabilities", "topics": [ "calc_genoprob" ] }, { "page": "calc_grid", "title": "Calculate indicators of which marker/pseudomarker positions are along a fixed grid", "topics": [ "calc_grid" ] }, { "page": "calc_het", "title": "Calculate heterozygosities", "topics": [ "calc_het" ] }, { "page": "calc_hotspots", "title": "Calculate QTL hotspots", "topics": [ "calc_hotspots" ] }, { "page": "calc_kinship", "title": "Calculate kinship matrix", "topics": [ "calc_kinship" ] }, { "page": "calc_raw_founder_maf", "title": "Calculate founder minor allele frequencies from raw SNP genotypes", "topics": [ "calc_raw_founder_maf" ] }, { "page": "calc_raw_geno_freq", "title": "Calculate genotype frequencies from raw SNP genotypes", "topics": [ "calc_raw_geno_freq" ] }, { "page": "calc_raw_het", "title": "Calculate estimated heterozygosity from raw SNP genotypes", "topics": [ "calc_raw_het" ] }, { "page": "calc_raw_maf", "title": "Calculate minor allele frequency from raw SNP genotypes", "topics": [ "calc_raw_maf" ] }, { "page": "calc_sdp", "title": "Calculate strain distribution pattern from SNP genotypes", "topics": [ "calc_sdp" ] }, { "page": "cbind_expand", "title": "Combine matrices by columns, expanding and aligning rows", "topics": [ "cbind_expand" ] }, { "page": "cbind.calc_genoprob", "title": "Join genotype probabilities for different chromosomes", "topics": [ "cbind.calc_genoprob" ] }, { "page": "cbind.phasedgeno", "title": "Join phased genotype results for different chromosomes", "topics": [ "cbind.phasedgeno" ] }, { "page": "cbind.scan1", "title": "Join genome scan results for different phenotypes.", "topics": [ "cbind.scan1" ] }, { "page": "cbind.scan1perm", "title": "Combine columns from multiple scan1 permutation results", "topics": [ "cbind.scan1perm" ] }, { "page": "cbind.sim_geno", "title": "Join genotype imputations for different chromosomes", "topics": [ "cbind.sim_geno" ] }, { "page": "cbind.viterbi", "title": "Join viterbi results for different chromosomes", "topics": [ "cbind.viterbi" ] }, { "page": "CCcolors", "title": "Collaborative Cross colors", "topics": [ "CCaltcolors", "CCcolors", "CCorigcolors" ] }, { "page": "check_cross2", "title": "Check a cross2 object", "topics": [ "check_cross2" ] }, { "page": "chisq_colpairs", "title": "Chi-square test on all pairs of columns", "topics": [ "chisq_colpairs" ] }, { "page": "chr_lengths", "title": "Calculate chromosome lengths", "topics": [ "chr_lengths" ] }, { "page": "clean", "title": "Clean an object", "topics": [ "clean" ] }, { "page": "clean_genoprob", "title": "Clean genotype probabilities", "topics": [ "clean.calc_genoprob", "clean_genoprob" ] }, { "page": "clean_scan1", "title": "Clean scan1 output", "topics": [ "clean.scan1", "clean_scan1" ] }, { "page": "compare_founder_geno", "title": "Compare founders genotype data", "topics": [ "compare_founder_geno" ] }, { "page": "compare_geno", "title": "Compare individuals' genotype data", "topics": [ "compare_geno" ] }, { "page": "compare_genoprob", "title": "Compare two sets of genotype probabilities", "topics": [ "compare_genoprob" ] }, { "page": "compare_maps", "title": "Compare two marker maps", "topics": [ "compare_maps" ] }, { "page": "convert2cross2", "title": "Convert R/qtl cross object to new format", "topics": [ "convert2cross2" ] }, { "page": "count_xo", "title": "Count numbers of crossovers", "topics": [ "count_xo" ] }, { "page": "create_gene_query_func", "title": "Create a function to query genes", "topics": [ "create_gene_query_func" ] }, { "page": "create_snpinfo", "title": "Create snp information table for a cross", "topics": [ "create_snpinfo" ] }, { "page": "create_variant_query_func", "title": "Create a function to query variants", "topics": [ "create_variant_query_func" ] }, { "page": "decomp_kinship", "title": "Calculate eigen decomposition of kinship matrix", "topics": [ "decomp_kinship" ] }, { "page": "drop_markers", "title": "Drop markers from a cross2 object", "topics": [ "drop_markers" ] }, { "page": "drop_nullmarkers", "title": "Drop markers with no genotype data", "topics": [ "drop_nullmarkers" ] }, { "page": "est_herit", "title": "Estimate heritability with a linear mixed model", "topics": [ "est_herit" ] }, { "page": "est_map", "title": "Estimate genetic maps", "topics": [ "est_map" ] }, { "page": "find_dup_markers", "title": "Find markers with identical genotype data", "topics": [ "find_dup_markers" ] }, { "page": "find_ibd_segments", "title": "Find IBD segments for a set of strains", "topics": [ "find_ibd_segments" ] }, { "page": "find_index_snp", "title": "Find name of indexed snp", "topics": [ "find_index_snp" ] }, { "page": "find_map_gaps", "title": "Find gaps in a genetic map", "topics": [ "find_map_gaps" ] }, { "page": "find_marker", "title": "Find markers by chromosome position", "topics": [ "find_marker" ] }, { "page": "find_markerpos", "title": "Find positions of markers", "topics": [ "find_markerpos" ] }, { "page": "find_peaks", "title": "Find peaks in a set of LOD curves", "topics": [ "find_peaks" ] }, { "page": "fit1", "title": "Fit single-QTL model at a single position", "topics": [ "fit1" ] }, { "page": "fread_csv", "title": "Read a csv file", "topics": [ "fread_csv" ] }, { "page": "fread_csv_numer", "title": "Read a csv file that has numeric columns", "topics": [ "fread_csv_numer" ] }, { "page": "genoprob_to_alleleprob", "title": "Convert genotype probabilities to allele probabilities", "topics": [ "genoprob_to_alleleprob" ] }, { "page": "genoprob_to_snpprob", "title": "Convert genotype probabilities to SNP probabilities", "topics": [ "genoprob_to_snpprob" ] }, { "page": "get_common_ids", "title": "Get common set of IDs from objects", "topics": [ "get_common_ids" ] }, { "page": "get_x_covar", "title": "Get X chromosome covariates", "topics": [ "get_x_covar" ] }, { "page": "guess_phase", "title": "Guess phase of imputed genotypes", "topics": [ "guess_phase" ] }, { "page": "index_snps", "title": "Create index of equivalent SNPs", "topics": [ "index_snps" ] }, { "page": "insert_pseudomarkers", "title": "Insert pseudomarkers into a marker map", "topics": [ "insert_pseudomarkers" ] }, { "page": "interp_genoprob", "title": "Interpolate genotype probabilities", "topics": [ "interp_genoprob" ] }, { "page": "interp_map", "title": "Interpolate between maps", "topics": [ "interp_map" ] }, { "page": "invert_sdp", "title": "Calculate SNP genotype matrix from strain distribution patterns", "topics": [ "invert_sdp" ] }, { "page": "locate_xo", "title": "Locate crossovers", "topics": [ "locate_xo" ] }, { "page": "lod_int", "title": "Calculate LOD support intervals", "topics": [ "lod_int" ] }, { "page": "map_to_grid", "title": "Subset a map to positions on a grid", "topics": [ "map_to_grid" ] }, { "page": "mat2strata", "title": "Define strata based on rows of a matrix", "topics": [ "mat2strata" ] }, { "page": "max_compare_geno", "title": "Find pair with most similar genotypes", "topics": [ "max.compare_geno", "max_compare_geno" ] }, { "page": "max_scan1", "title": "Find position with maximum LOD score", "topics": [ "max.scan1", "max_scan1" ] }, { "page": "maxlod", "title": "Overall maximum LOD score", "topics": [ "maxlod" ] }, { "page": "maxmarg", "title": "Find genotypes with maximum marginal probabilities", "topics": [ "maxmarg" ] }, { "page": "n_missing", "title": "Count missing genotypes", "topics": [ "n_missing", "n_typed" ] }, { "page": "plot_ci", "title": "Effect plot with multiple CIs for different groups", "topics": [ "plot_ci" ] }, { "page": "plot_cistrans", "title": "cis-trans plot for eQTL results", "topics": [ "plot_cistrans" ] }, { "page": "plot_coef", "title": "Plot QTL effects along chromosome", "topics": [ "plot.scan1coef", "plot_coef", "plot_coefCC" ] }, { "page": "plot_colorscale", "title": "Heat map color scale", "topics": [ "plot_colorscale" ] }, { "page": "plot_compare_geno", "title": "Plot of compare_geno object.", "topics": [ "plot.compare_geno", "plot_compare_geno" ] }, { "page": "plot_genes", "title": "Plot gene locations for a genomic interval", "topics": [ "plot_genes" ] }, { "page": "plot_geno", "title": "Plot multiple individuals' genome-wide genotypes", "topics": [ "plot_geno" ] }, { "page": "plot_genoprob", "title": "Plot genotype probabilities for one individual on one chromosome.", "topics": [ "plot.calc_genoprob", "plot_genoprob" ] }, { "page": "plot_genoprobcomp", "title": "Plot comparison of two sets of genotype probabilities", "topics": [ "plot_genoprobcomp" ] }, { "page": "plot_lodpeaks", "title": "Plot LOD scores vs QTL peak locations", "topics": [ "plot_lodpeaks" ] }, { "page": "plot_onegeno", "title": "Plot one individual's genome-wide genotypes", "topics": [ "plot_onegeno" ] }, { "page": "plot_peaks", "title": "Plot QTL peak locations", "topics": [ "plot_peaks" ] }, { "page": "plot_pxg", "title": "Plot phenotype vs genotype", "topics": [ "plot_pxg" ] }, { "page": "plot_scan1", "title": "Plot a genome scan", "topics": [ "plot.scan1", "plot_scan1" ] }, { "page": "plot_scan1_heatmap", "title": "Heat map of scan1 results with multiple traits", "topics": [ "plot_scan1_heatmap" ] }, { "page": "plot_sdp", "title": "plot strain distribution patterns for SNPs", "topics": [ "plot_sdp" ] }, { "page": "plot_snpasso", "title": "Plot SNP associations", "topics": [ "plot_snpasso" ] }, { "page": "predict_snpgeno", "title": "Predict SNP genotypes", "topics": [ "predict_snpgeno" ] }, { "page": "print.cross2", "title": "Print a cross2 object", "topics": [ "print.cross2" ] }, { "page": "print.summary.scan1perm", "title": "Print summary of scan1perm permutations", "topics": [ "print.summary.scan1perm" ] }, { "page": "probs_to_grid", "title": "Subset genotype probability array to pseudomarkers on a grid", "topics": [ "probs_to_grid" ] }, { "page": "pull_genoprobint", "title": "Pull genotype probabilities for an interval", "topics": [ "pull_genoprobint" ] }, { "page": "pull_genoprobpos", "title": "Pull genotype probabilities for a particular position", "topics": [ "pull_genoprobpos" ] }, { "page": "pull_markers", "title": "Drop all but a specified set of markers", "topics": [ "pull_markers" ] }, { "page": "qtl2version", "title": "Installed version of R/qtl2", "topics": [ "qtl2version" ] }, { "page": "rbind.calc_genoprob", "title": "Join genotype probabilities for different individuals", "topics": [ "rbind.calc_genoprob" ] }, { "page": "rbind.phasedgeno", "title": "Join phased geno results for different individuals", "topics": [ "rbind.phasedgeno" ] }, { "page": "rbind.scan1", "title": "Join genome scan results for different chromosomes.", "topics": [ "rbind.scan1" ] }, { "page": "rbind.scan1perm", "title": "Combine data from scan1perm objects", "topics": [ "c.scan1perm", "rbind.scan1perm" ] }, { "page": "rbind.sim_geno", "title": "Join genotype imputations for different individuals", "topics": [ "rbind.sim_geno" ] }, { "page": "rbind.viterbi", "title": "Join Viterbi results for different individuals", "topics": [ "rbind.viterbi" ] }, { "page": "read_cross2", "title": "Read QTL data from files", "topics": [ "read_cross2" ] }, { "page": "read_pheno", "title": "Read phenotype data", "topics": [ "read_pheno" ] }, { "page": "recode_snps", "title": "Recode SNPs by major allele", "topics": [ "recode_snps" ] }, 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