| Add thresholds to genome scan plot | add_threshold |
| Basic summaries of a cross2 object | 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 |
| Batch columns by pattern of missing values | batch_cols |
| Split vector into batches | batch_vec |
| Calculate Bayes credible intervals | bayes_int |
| Calculate entropy of genotype probability distribution | calc_entropy |
| Calculate genotyping error LOD scores | calc_errorlod |
| Calculate genotype frequencies | calc_geno_freq |
| Calculate conditional genotype probabilities | calc_genoprob |
| Calculate indicators of which marker/pseudomarker positions are along a fixed grid | calc_grid |
| Calculate heterozygosities | calc_het |
| Calculate kinship matrix | calc_kinship |
| Calculate founder minor allele frequencies from raw SNP genotypes | calc_raw_founder_maf |
| Calculate genotype frequencies from raw SNP genotypes | calc_raw_geno_freq |
| Calculate estimated heterozygosity from raw SNP genotypes | calc_raw_het |
| Calculate minor allele frequency from raw SNP genotypes | calc_raw_maf |
| Calculate strain distribution pattern from SNP genotypes | calc_sdp |
| Combine matrices by columns, expanding and aligning rows | cbind_expand |
| Join genotype probabilities for different chromosomes | cbind.calc_genoprob |
| Join genome scan results for different phenotypes. | cbind.scan1 |
| Combine columns from multiple scan1 permutation results | cbind.scan1perm |
| Join genotype imputations for different chromosomes | cbind.sim_geno |
| Join viterbi results for different chromosomes | cbind.viterbi |
| Collaborative Cross colors | CCaltcolors CCcolors CCorigcolors |
| Check a cross2 object | check_cross2 |
| Chi-square test on all pairs of columns | chisq_colpairs |
| Calculate chromosome lengths | chr_lengths |
| Clean an object | clean |
| Clean genotype probabilities | clean.calc_genoprob clean_genoprob |
| Clean scan1 output | clean.scan1 clean_scan1 |
| Compare individuals' genotype data | compare_geno |
| Compare two sets of genotype probabilities | compare_genoprob |
| Compare two marker maps | compare_maps |
| Convert R/qtl cross object to new format | convert2cross2 |
| Count numbers of crossovers | count_xo |
| Create a function to query genes | create_gene_query_func |
| Create snp information table for a cross | create_snpinfo |
| Create a function to query variants | create_variant_query_func |
| Calculate eigen decomposition of kinship matrix | decomp_kinship |
| Drop markers from a cross2 object | drop_markers |
| Drop markers with no genotype data | drop_nullmarkers |
| Estimate heritability with a linear mixed model | est_herit |
| Estimate genetic maps | est_map |
| Find markers with identical genotype data | find_dup_markers |
| Find IBD segments for a set of strains | find_ibd_segments |
| Find name of indexed snp | find_index_snp |
| Find gaps in a genetic map | find_map_gaps |
| Find markers by chromosome position | find_marker |
| Find positions of markers | find_markerpos |
| Find peaks in a set of LOD curves | find_peaks |
| Fit single-QTL model at a single position | fit1 |
| Read a csv file | fread_csv |
| Read a csv file that has numeric columns | fread_csv_numer |
| Convert genotype probabilities to allele probabilities | genoprob_to_alleleprob |
| Convert genotype probabilities to SNP probabilities | genoprob_to_snpprob |
| Get common set of IDs from objects | get_common_ids |
| Get X chromosome covariates | get_x_covar |
| Guess phase of imputed genotypes | guess_phase |
| Create index of equivalent SNPs | index_snps |
| Insert pseudomarkers into a marker map | insert_pseudomarkers |
| Interpolate genotype probabilities | interp_genoprob |
| Interpolate between maps | interp_map |
| Calculate SNP genotype matrix from strain distribution patterns | invert_sdp |
| Locate crossovers | locate_xo |
| Calculate LOD support intervals | lod_int |
| Subset a map to positions on a grid | map_to_grid |
| Define strata based on rows of a matrix | mat2strata |
| Find pair with most similar genotypes | max.compare_geno max_compare_geno |
| Find position with maximum LOD score | max.scan1 max_scan1 |
| Overall maximum LOD score | maxlod |
| Find genotypes with maximum marginal probabilities | maxmarg |
| Count missing genotypes | n_missing n_typed |
| Plot QTL effects along chromosome | plot.scan1coef plot_coef plot_coefCC |
| Plot of compare_geno object. | plot.compare_geno plot_compare_geno |
| Plot gene locations for a genomic interval | plot_genes |
| Plot genotype probabilities for one individual on one chromosome. | plot.calc_genoprob plot_genoprob |
| Plot comparison of two sets of genotype probabilities | plot_genoprobcomp |
| Plot LOD scores vs QTL peak locations | plot_lodpeaks |
| Plot one individual's genome-wide genotypes | plot_onegeno |
| Plot QTL peak locations | plot_peaks |
| Plot phenotype vs genotype | plot_pxg |
| Plot a genome scan | plot.scan1 plot_scan1 |
| plot strain distribution patterns for SNPs | plot_sdp |
| Plot SNP associations | plot_snpasso |
| Predict SNP genotypes | predict_snpgeno |
| Print a cross2 object | print.cross2 |
| Print summary of scan1perm permutations | print.summary.scan1perm |
| Subset genotype probability array to pseudomarkers on a grid | probs_to_grid |
| Pull genotype probabilities for an interval | pull_genoprobint |
| Pull genotype probabilities for a particular position | pull_genoprobpos |
| Drop all but a specified set of markers | pull_markers |
| Installed version of R/qtl2 | qtl2version |
| Join genotype probabilities for different individuals | rbind.calc_genoprob |
| Join genome scan results for different chromosomes. | rbind.scan1 |
| Combine data from scan1perm objects | c.scan1perm rbind.scan1perm |
| Join genotype imputations for different individuals | rbind.sim_geno |
| Join Viterbi results for different individuals | rbind.viterbi |
| Read QTL data from files | read_cross2 |
| Read phenotype data | read_pheno |
| Recode SNPs by major allele | recode_snps |
| Reduce the lengths of gaps in a map | reduce_map_gaps |
| Reduce markers to a subset of more-evenly-spaced ones | reduce_markers |
| Replace individual IDs | replace_ids replace_ids.calc_genoprob replace_ids.cross2 replace_ids.data.frame replace_ids.matrix replace_ids.sim_geno replace_ids.viterbi |
| Scale kinship matrix | scale_kinship |
| Genome scan with a single-QTL model | scan1 |
| Calculate BLUPs of QTL effects in scan along one chromosome | scan1blup |
| Calculate QTL effects in scan along one chromosome | scan1coef |
| Maximum LOD score from genome scan with a single-QTL model | scan1max |
| Permutation test for genome scan with a single-QTL model | scan1perm |
| Single-QTL genome scan at imputed SNPs | scan1snps |
| Convert strain distribution patterns to character strings | sdp2char |
| Simulate genotypes given observed marker data | sim_geno |
| Smooth genetic map | smooth_gmap |
| Subset scan1 output | subset.scan1 subset_scan1 |
| Subsetting genotype probabilities | subset.calc_genoprob [.calc_genoprob |
| Subsetting data for a QTL experiment | subset.cross2 [.cross2 |
| Subsetting imputed genotypes | subset.sim_geno [.sim_geno |
| Subsetting Viterbi results | subset.viterbi [.viterbi |
| Basic summary of compare_geno object | print.summary.compare_geno summary.compare_geno summary_compare_geno |
| Summarize scan1perm results | summary.scan1perm summary_scan1perm |
| Summary of cross2 object | summary.cross2 |
| Create table of top snp associations | top_snps |
| Unsmooth genetic map | unsmooth_gmap |
| Calculate most probable sequence of genotypes | viterbi |
| Write a control file for QTL data | write_control_file |
| Get x-axis position for genomic location | xpos_scan1 |
| Zip a set of data files | zip_datafiles |
