Quantitative Trait Locus Mapping in Experimental Crosses
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Documentation for package ‘qtl2’ version 0.42
Help Pages
A B C D E F G I L M N P Q R S T U V W X Z misc
-- A --
| add_threshold | Add thresholds to genome scan plot |
-- B --
| basic_summaries | Basic summaries of a cross2 object |
| batch_cols | Batch columns by pattern of missing values |
| batch_vec | Split vector into batches |
| bayes_int | Calculate Bayes credible intervals |
-- C --
| c.scan1perm | Combine data from scan1perm objects |
| calc_entropy | Calculate entropy of genotype probability distribution |
| calc_errorlod | Calculate genotyping error LOD scores |
| calc_genoprob | Calculate conditional genotype probabilities |
| calc_geno_freq | Calculate genotype frequencies |
| calc_grid | Calculate indicators of which marker/pseudomarker positions are along a fixed grid |
| calc_het | Calculate heterozygosities |
| calc_hotspots | Calculate QTL hotspots |
| calc_kinship | Calculate kinship matrix |
| calc_raw_founder_maf | Calculate founder minor allele frequencies from raw SNP genotypes |
| calc_raw_geno_freq | Calculate genotype frequencies from raw SNP genotypes |
| calc_raw_het | Calculate estimated heterozygosity from raw SNP genotypes |
| calc_raw_maf | Calculate minor allele frequency from raw SNP genotypes |
| calc_sdp | Calculate strain distribution pattern from SNP genotypes |
| cbind.calc_genoprob | Join genotype probabilities for different chromosomes |
| cbind.phasedgeno | Join phased genotype results for different chromosomes |
| cbind.scan1 | Join genome scan results for different phenotypes. |
| cbind.scan1perm | Combine columns from multiple scan1 permutation results |
| cbind.sim_geno | Join genotype imputations for different chromosomes |
| cbind.viterbi | Join viterbi results for different chromosomes |
| cbind_expand | Combine matrices by columns, expanding and aligning rows |
| CCaltcolors | Collaborative Cross colors |
| CCcolors | Collaborative Cross colors |
| CCorigcolors | Collaborative Cross colors |
| check_cross2 | Check a cross2 object |
| chisq_colpairs | Chi-square test on all pairs of columns |
| chr_lengths | Calculate chromosome lengths |
| chr_names | Basic summaries of a cross2 object |
| clean | Clean an object |
| clean.calc_genoprob | Clean genotype probabilities |
| clean.scan1 | Clean scan1 output |
| clean_genoprob | Clean genotype probabilities |
| clean_scan1 | Clean scan1 output |
| compare_founder_geno | Compare founders genotype data |
| compare_geno | Compare individuals' genotype data |
| compare_genoprob | Compare two sets of genotype probabilities |
| compare_maps | Compare two marker maps |
| convert2cross2 | Convert R/qtl cross object to new format |
| count_xo | Count numbers of crossovers |
| covar_names | Basic summaries of a cross2 object |
| create_gene_query_func | Create a function to query genes |
| create_snpinfo | Create snp information table for a cross |
| create_variant_query_func | Create a function to query variants |
-- D --
| decomp_kinship | Calculate eigen decomposition of kinship matrix |
| drop_markers | Drop markers from a cross2 object |
| drop_nullmarkers | Drop markers with no genotype data |
-- E --
| est_herit | Estimate heritability with a linear mixed model |
| est_map | Estimate genetic maps |
-- F --
| find_dup_markers | Find markers with identical genotype data |
| find_ibd_segments | Find IBD segments for a set of strains |
| find_index_snp | Find name of indexed snp |
| find_map_gaps | Find gaps in a genetic map |
| find_marker | Find markers by chromosome position |
| find_markerpos | Find positions of markers |
| find_peaks | Find peaks in a set of LOD curves |
| fit1 | Fit single-QTL model at a single position |
| founders | Basic summaries of a cross2 object |
| fread_csv | Read a csv file |
| fread_csv_numer | Read a csv file that has numeric columns |
-- G --
| genoprob_to_alleleprob | Convert genotype probabilities to allele probabilities |
| genoprob_to_snpprob | Convert genotype probabilities to SNP probabilities |
| get_common_ids | Get common set of IDs from objects |
| get_x_covar | Get X chromosome covariates |
| guess_phase | Guess phase of imputed genotypes |
-- I --
| index_snps | Create index of equivalent SNPs |
| ind_ids | Basic summaries of a cross2 object |
| ind_ids_covar | Basic summaries of a cross2 object |
| ind_ids_geno | Basic summaries of a cross2 object |
| ind_ids_gnp | Basic summaries of a cross2 object |
| ind_ids_pheno | Basic summaries of a cross2 object |
| insert_pseudomarkers | Insert pseudomarkers into a marker map |
| interp_genoprob | Interpolate genotype probabilities |
| interp_map | Interpolate between maps |
| invert_sdp | Calculate SNP genotype matrix from strain distribution patterns |
-- L --
| locate_xo | Locate crossovers |
| lod_int | Calculate LOD support intervals |
-- M --
| map_to_grid | Subset a map to positions on a grid |
| marker_names | Basic summaries of a cross2 object |
| mat2strata | Define strata based on rows of a matrix |
| max.compare_geno | Find pair with most similar genotypes |
| max.scan1 | Find position with maximum LOD score |
| maxlod | Overall maximum LOD score |
| maxmarg | Find genotypes with maximum marginal probabilities |
| max_compare_geno | Find pair with most similar genotypes |
| max_scan1 | Find position with maximum LOD score |
-- N --
| n_chr | Basic summaries of a cross2 object |
| n_covar | Basic summaries of a cross2 object |
| n_founders | Basic summaries of a cross2 object |
| n_ind | Basic summaries of a cross2 object |
| n_ind_covar | Basic summaries of a cross2 object |
| n_ind_geno | Basic summaries of a cross2 object |
| n_ind_gnp | Basic summaries of a cross2 object |
| n_ind_pheno | Basic summaries of a cross2 object |
| n_mar | Basic summaries of a cross2 object |
| n_missing | Count missing genotypes |
| n_pheno | Basic summaries of a cross2 object |
| n_phenocovar | Basic summaries of a cross2 object |
| n_typed | Count missing genotypes |
-- P --
| phenocovar_names | Basic summaries of a cross2 object |
| pheno_names | Basic summaries of a cross2 object |
| plot.calc_genoprob | Plot genotype probabilities for one individual on one chromosome. |
| plot.compare_geno | Plot of compare_geno object. |
| plot.scan1 | Plot a genome scan |
| plot.scan1coef | Plot QTL effects along chromosome |
| plot_ci | Effect plot with multiple CIs for different groups |
| plot_cistrans | cis-trans plot for eQTL results |
| plot_coef | Plot QTL effects along chromosome |
| plot_coefCC | Plot QTL effects along chromosome |
| plot_colorscale | Heat map color scale |
| plot_compare_geno | Plot of compare_geno object. |
| plot_genes | Plot gene locations for a genomic interval |
| plot_geno | Plot multiple individuals' genome-wide genotypes |
| plot_genoprob | Plot genotype probabilities for one individual on one chromosome. |
| plot_genoprobcomp | Plot comparison of two sets of genotype probabilities |
| plot_lodpeaks | Plot LOD scores vs QTL peak locations |
| plot_onegeno | Plot one individual's genome-wide genotypes |
| plot_peaks | Plot QTL peak locations |
| plot_pxg | Plot phenotype vs genotype |
| plot_scan1 | Plot a genome scan |
| plot_scan1_heatmap | Heat map of scan1 results with multiple traits |
| plot_sdp | plot strain distribution patterns for SNPs |
| plot_snpasso | Plot SNP associations |
| predict_snpgeno | Predict SNP genotypes |
| print.cross2 | Print a cross2 object |
| print.summary.compare_geno | Basic summary of compare_geno object |
| print.summary.scan1perm | Print summary of scan1perm permutations |
| probs_to_grid | Subset genotype probability array to pseudomarkers on a grid |
| pull_genoprobint | Pull genotype probabilities for an interval |
| pull_genoprobpos | Pull genotype probabilities for a particular position |
| pull_markers | Drop all but a specified set of markers |
-- Q --
| qtl2version | Installed version of R/qtl2 |
-- R --
| rbind.calc_genoprob | Join genotype probabilities for different individuals |
| rbind.phasedgeno | Join phased geno results for different individuals |
| rbind.scan1 | Join genome scan results for different chromosomes. |
| rbind.scan1perm | Combine data from scan1perm objects |
| rbind.sim_geno | Join genotype imputations for different individuals |
| rbind.viterbi | Join Viterbi results for different individuals |
| read_cross2 | Read QTL data from files |
| read_pheno | Read phenotype data |
| recode_snps | Recode SNPs by major allele |
| reduce_map_gaps | Reduce the lengths of gaps in a map |
| reduce_markers | Reduce markers to a subset of more-evenly-spaced ones |
| replace_ids | Replace individual IDs |
| replace_ids.calc_genoprob | Replace individual IDs |
| replace_ids.cross2 | Replace individual IDs |
| replace_ids.data.frame | Replace individual IDs |
| replace_ids.matrix | Replace individual IDs |
| replace_ids.sim_geno | Replace individual IDs |
| replace_ids.viterbi | Replace individual IDs |
-- S --
| scale_kinship | Scale kinship matrix |
| scan1 | Genome scan with a single-QTL model |
| scan1blup | Calculate BLUPs of QTL effects in scan along one chromosome |
| scan1coef | Calculate QTL effects in scan along one chromosome |
| scan1max | Maximum LOD score from genome scan with a single-QTL model |
| scan1perm | Permutation test for genome scan with a single-QTL model |
| scan1snps | Single-QTL genome scan at imputed SNPs |
| sdp2char | Convert strain distribution patterns to character strings |
| sim_geno | Simulate genotypes given observed marker data |
| smooth_gmap | Smooth genetic map |
| subset.calc_genoprob | Subsetting genotype probabilities |
| subset.cross2 | Subsetting data for a QTL experiment |
| subset.phasedgeno | Subsetting phased genotype objects |
| subset.scan1 | Subset scan1 output |
| subset.sim_geno | Subsetting imputed genotypes |
| subset.viterbi | Subsetting Viterbi results |
| subset_scan1 | Subset scan1 output |
| summary.compare_geno | Basic summary of compare_geno object |
| summary.cross2 | Summary of cross2 object |
| summary.scan1perm | Summarize scan1perm results |
| summary_compare_geno | Basic summary of compare_geno object |
| summary_scan1perm | Summarize scan1perm results |
-- T --
| top_snps | Create table of top snp associations |
| tot_mar | Basic summaries of a cross2 object |
-- U --
| unsmooth_gmap | Unsmooth genetic map |
-- V --
| viterbi | Calculate most probable sequence of genotypes |
-- W --
| write_control_file | Write a control file for QTL data |
-- X --
| xpos_scan1 | Get x-axis position for genomic location |
-- Z --
| zip_datafiles | Zip a set of data files |
-- misc --
| [.calc_genoprob | Subsetting genotype probabilities |
| [.cross2 | Subsetting data for a QTL experiment |
| [.phasedgeno | Subsetting phased genotype objects |
| [.sim_geno | Subsetting imputed genotypes |
| [.viterbi | Subsetting Viterbi results |