API for qtl2
Quantitative Trait Locus Mapping in Experimental Crosses
| Global functions | |
|---|---|
| .Xgenoprob_to_snpprob | Source code |
| .alleleprob_to_snpprob | Source code |
| .bayes_int_plain | Source code |
| .calc_errorlod | Source code |
| .calc_genoprob | Source code |
| .calc_genoprob2 | Source code |
| .calc_kinship | Source code |
| .calc_sdp | Source code |
| .check_crossinfo | Source code |
| .check_is_female_vector | Source code |
| .chisq_colpairs | Source code |
| .clean_genoprob | Source code |
| .compare_geno | Source code |
| .count_invalid_genotypes | Source code |
| .count_xo | Source code |
| .count_xo_3d | Source code |
| .crosstype_supported | Source code |
| .est_map | Source code |
| .est_map2 | Source code |
| .find_ibd_segments | Source code |
| .find_peaks | Source code |
| .find_peaks_and_bayesint | Source code |
| .find_peaks_and_lodint | Source code |
| .genoprob_to_alleleprob | Source code |
| .genoprob_to_snpprob | Source code |
| .get_x_covar | Source code |
| .guess_phase_A | Source code |
| .guess_phase_X | Source code |
| .guess_phase_f2A | Source code |
| .guess_phase_f2X | Source code |
| .interp_genoprob_onechr | Source code |
| .invert_sdp | Source code |
| .is_phase_known | Source code |
| .locate_xo | Source code |
| .lod_int_plain | Source code |
| .maxmarg | Source code |
| .predict_snpgeno | Source code |
| .reduce_markers | Source code |
| .sim_geno | Source code |
| .sim_geno2 | Source code |
| .viterbi | Source code |
| .viterbi2 | Source code |
| CCaltcolors | Man page |
| CCcolors | Man page |
| CCorigcolors | Man page |
| Rcpp_calcLL | Source code |
| Rcpp_calcLL_mat | Source code |
| Rcpp_calc_logdetXpX | Source code |
| Rcpp_eigen_decomp | Source code |
| Rcpp_eigen_rotation | Source code |
| Rcpp_fitLMM | Source code |
| Rcpp_fitLMM_mat | Source code |
| Xgenocol_to_snpcol | Source code |
| [.calc_genoprob | Man page |
| [.cross2 | Man page |
| [.sim_geno | Man page |
| [.viterbi | Man page |
| `[.calc_genoprob` | Source code |
| `[.cross2` | Source code |
| `[.sim_geno` | Source code |
| `[.viterbi` | Source code |
| add_lod_labels | Source code |
| add_threshold | Man page Source code |
| addgenorect | Source code |
| addlog | Source code |
| align_geno_sex_cross | Source code |
| align_scan1_map | Man page Source code |
| any_duplicates | Source code |
| arrange_genes | Source code |
| assign_allele_codes | Source code |
| basic_summaries | Man page |
| batch_cols | Man page Source code |
| batch_vec | Man page Source code |
| bayes_int | Man page Source code |
| c.scan1perm | Man page |
| calc_coefSE_binreg | Source code |
| calc_coefSE_binreg_eigenqr | Source code |
| calc_coefSE_binreg_weighted | Source code |
| calc_coefSE_binreg_weighted_eigenqr | Source code |
| calc_coefSE_linreg | Source code |
| calc_coefSE_linreg_eigenchol | Source code |
| calc_coefSE_linreg_eigenqr | Source code |
| calc_coef_binreg | Source code |
| calc_coef_binreg_eigenqr | Source code |
| calc_coef_binreg_weighted | Source code |
| calc_coef_binreg_weighted_eigenqr | Source code |
| calc_coef_linreg | Source code |
| calc_coef_linreg_eigenchol | Source code |
| calc_coef_linreg_eigenqr | Source code |
| calc_entropy | Man page Source code |
| calc_errorlod | Man page Source code |
| calc_fitted_linreg_eigenchol | Source code |
| calc_fitted_linreg_eigenqr | Source code |
| calc_geno_freq | Man page Source code |
| calc_genoprob | Man page Source code |
| calc_genoprob2 | Source code |
| calc_grid | Man page Source code |
| calc_grid_onechr | Source code |
| calc_het | Man page Source code |
| calc_hsq_clean | Source code |
| calc_kinship | Man page Source code |
| calc_kinship_bychr | Source code |
| calc_kinship_overall | Source code |
| calc_ll_binreg | Source code |
| calc_ll_binreg_eigenchol | Source code |
| calc_ll_binreg_eigenqr | Source code |
| calc_ll_binreg_weighted | Source code |
| calc_ll_binreg_weighted_eigenchol | Source code |
| calc_ll_binreg_weighted_eigenqr | Source code |
| calc_mvrss_eigenchol | Source code |
| calc_mvrss_eigenqr | Source code |
| calc_nullLL_clean | Source code |
| calc_raw_founder_maf | Man page Source code |
| calc_raw_geno_freq | Man page Source code |
| calc_raw_het | Man page Source code |
| calc_raw_maf | Man page Source code |
| calc_resid_eigenchol | Source code |
| calc_resid_eigenqr | Source code |
| calc_resid_linreg | Source code |
| calc_resid_linreg_3d | Source code |
| calc_rss_eigenchol | Source code |
| calc_rss_eigenqr | Source code |
| calc_rss_linreg | Source code |
| calc_sdp | Man page Source code |
| cbind.calc_genoprob | Man page Source code |
| cbind.scan1 | Man page Source code |
| cbind.scan1perm | Man page Source code |
| cbind.sim_geno | Man page Source code |
| cbind.viterbi | Man page Source code |
| cbind_expand | Man page Source code |
| cbind_expand_noalign | Source code |
| check4duplicates | Source code |
| check4names | Source code |
| check_binary_pheno | Source code |
| check_cross2 | Man page Source code |
| check_crossinfo | Source code |
| check_crosstype | Source code |
| check_extra_dots | Source code |
| check_founder_geno_size | Source code |
| check_handle_x_chr | Source code |
| check_is_female_vector | Source code |
| check_kinship | Source code |
| check_kinship_onechr | Source code |
| check_new_ids | Source code |
| chisq_colpairs | Man page Source code |
| chr_lengths | Man page Source code |
| chr_names | Man page Source code |
| clean | Man page Source code |
| clean.calc_genoprob | Man page |
| clean.scan1 | Man page |
| clean_genoprob | Man page Source code |
| clean_scan1 | Man page Source code |
| cluster_lapply | Source code |
| collapse_chr_lengths_to_AX | Source code |
| colnames4attr | Source code |
| combine_markers_with_pseudomarkers | Source code |
| compare_geno | Man page Source code |
| compare_genoprob | Man page Source code |
| compare_genoprob_add_annotation | Source code |
| compare_maps | Man page Source code |
| convert2cross2 | Man page Source code |
| convert_cross_info | Source code |
| convert_sex | Source code |
| convert_sexcodes | Source code |
| count_invalid_genotypes | Source code |
| count_xo | Man page Source code |
| covar_names | Man page Source code |
| create_empty_founder_geno | Source code |
| create_gene_query_func | Man page Source code |
| create_marker_index | Source code |
| create_pseudomarker_names | Source code |
| create_snpinfo | Man page Source code |
| create_variant_query_func | Man page Source code |
| decomp_kinship | Man page Source code |
| dim.calc_genoprob | Source code |
| dimnames.calc_genoprob | Source code |
| double_kinship | Source code |
| drop_depcols | Source code |
| drop_incomplete_markers | Source code |
| drop_markers | Man page Source code |
| drop_nullmarkers | Man page Source code |
| drop_xcovar | Source code |
| est_herit | Man page Source code |
| est_map | Man page Source code |
| expand_genoprobs_intcovar | Source code |
| expand_interval_to_markers | Source code |
| expand_snp_results | Source code |
| extract_dim_from_header | Source code |
| find_common_ids | Source code |
| find_ibd_segments | Man page Source code |
| find_index_snp | Man page Source code |
| find_intervals | Source code |
| find_lin_indep_cols | Source code |
| find_map_gaps | Man page Source code |
| find_marker | Man page Source code |
| find_markerpos | Man page Source code |
| find_matching_cols | Source code |
| find_peaks | Man page Source code |
| find_peaks_and_bayesint | Source code |
| find_peaks_and_lodint | Source code |
| firstcol2rownames | Source code |
| fit1 | Man page Source code |
| fit1_binary_addcovar | Source code |
| fit1_binary_intcovar | Source code |
| fit1_hk_addcovar | Source code |
| fit1_hk_intcovar | Source code |
| fit1_pg | Source code |
| fit1_pg_addcovar | Source code |
| fit1_pg_intcovar | Source code |
| fit_binreg | Source code |
| fit_binreg_eigenqr | Source code |
| fit_binreg_weighted | Source code |
| fit_binreg_weighted_eigenqr | Source code |
| fit_linreg | Source code |
| fit_linreg_eigenchol | Source code |
| fit_linreg_eigenqr | Source code |
| force_intcovar | Source code |
| formX_intcovar | Source code |
| founders | Man page Source code |
| gen_strat_perm | Source code |
| geno2intervals | Source code |
| geno_names | Source code |
| genocol_to_snpcol | Source code |
| genoprob_to_alleleprob | Man page Source code |
| genoprob_to_snpprob | Man page Source code |
| genoprobs_by_contrasts | Source code |
| genoprobs_col2drop | Source code |
| get_common_ids | Man page Source code |
| get_permutation | Source code |
| get_x_covar | Man page Source code |
| grab_dots | Source code |
| guess_phase | Man page Source code |
| handle_null_crossinfo | Source code |
| handle_null_isfemale | Source code |
| handle_null_isxchr | Source code |
| hsq_dimnames | Source code |
| imf | Source code |
| imf.cf | Source code |
| imf.h | Source code |
| imf.k | Source code |
| imf.m | Source code |
| ind_ids | Man page Source code |
| ind_ids_covar | Man page Source code |
| ind_ids_geno | Man page Source code |
| ind_ids_gnp | Man page Source code |
| ind_ids_pheno | Man page Source code |
| index_batches_by_omits | Source code |
| index_snps | Man page Source code |
| infer_f1_geno | Source code |
| insert_pseudomarkers | Man page Source code |
| insert_pseudomarkers_grid | Source code |
| insert_pseudomarkers_minimal | Source code |
| insert_pseudomarkers_onechr | Source code |
| interp_genoprob | Man page Source code |
| interp_genoprob_onechr | Source code |
| interp_map | Man page Source code |
| interpolate_map | Source code |
| invert_founder_index | Source code |
| invert_sdp | Man page Source code |
| is.cross2 | Source code |
| is_cluster | Source code |
| is_kinship_decomposed | Source code |
| is_kinship_list | Source code |
| is_nonneg_number | Source code |
| is_null_weights | Source code |
| is_number | Source code |
| is_phase_known | Source code |
| is_pos_number | Source code |
| is_same | Source code |
| is_web_file | Source code |
| isnt_karl | Source code |
| kinship_bychr2loco | Source code |
| locate_xo | Man page Source code |
| lod_int | Man page Source code |
| map2chr | Source code |
| map2markernames | Source code |
| map2pos | Source code |
| map2rf | Source code |
| map_to_boundaries | Source code |
| map_to_grid | Man page Source code |
| map_to_index | Source code |
| map_to_xpos | Source code |
| marker_names | Man page Source code |
| mat2strata | Man page Source code |
| match_ids | Source code |
| matrix_x_3darray | Source code |
| matrix_x_matrix | Source code |
| matrix_x_vector | Source code |
| max.compare_geno | Man page |
| max.scan1 | Man page Source code |
| max_compare_geno | Man page Source code |
| max_scan1 | Man page Source code |
| maxall_scan1 | Source code |
| maxlod | Man page Source code |
| maxmarg | Man page Source code |
| mf | Source code |
| mf.cf | Source code |
| mf.h | Source code |
| mf.k | Source code |
| mf.m | Source code |
| mpp_decode_geno | Source code |
| mpp_encode_alleles | Source code |
| mpp_geno_names | Source code |
| mpp_is_het | Source code |
| myround | Source code |
| n_chr | Man page Source code |
| n_cores | Source code |
| n_covar | Man page Source code |
| n_founders | Man page Source code |
| n_ind | Man page Source code |
| n_ind_covar | Man page Source code |
| n_ind_geno | Man page Source code |
| n_ind_gnp | Man page Source code |
| n_ind_pheno | Man page Source code |
| n_mar | Man page Source code |
| n_missing | Man page Source code |
| n_pheno | Man page Source code |
| n_phenocovar | Man page Source code |
| n_typed | Man page Source code |
| nalleles | Source code |
| need_founder_geno | Source code |
| normalize_kinship | Source code |
| null_binary_clean | Source code |
| nullrss_clean | Source code |
| permute_ivector | Source code |
| permute_ivector_stratified | Source code |
| permute_nvector | Source code |
| permute_nvector_stratified | Source code |
| pheno2matrix | Source code |
| pheno_names | Man page Source code |
| phenocovar_names | Man page Source code |
| plot.calc_genoprob | Man page Source code |
| plot.compare_geno | Man page |
| plot.scan1 | Man page Source code |
| plot.scan1coef | Man page Source code |
| plot_coef | Man page Source code |
| plot_coefCC | Man page Source code |
| plot_coef_and_lod | Source code |
| plot_compare_geno | Man page Source code |
| plot_genes | Man page Source code |
| plot_genoprob | Man page Source code |
| plot_genoprob_internal | Source code |
| plot_genoprobcomp | Man page Source code |
| plot_lodpeaks | Man page Source code |
| plot_onegeno | Man page Source code |
| plot_peaks | Man page Source code |
| plot_pxg | Man page Source code |
| plot_scan1 | Man page Source code |
| plot_sdp | Man page Source code |
| plot_snpasso | Man page Source code |
| plot_snpasso_and_genes | Source code |
| plot_snpasso_and_sdp | Source code |
| plot_snpasso_sdp_genes | Source code |
| predict_snpgeno | Man page Source code |
| print.cross2 | Man page Source code |
| print.summary.compare_geno | Man page Source code |
| print.summary.cross2 | Source code |
| print.summary.scan1perm | Man page Source code |
| print_aligned | Source code |
| probs_to_grid | Man page Source code |
| pull_genoprobint | Man page Source code |
| pull_genoprobpos | Man page Source code |
| pull_markers | Man page Source code |
| qtl2 | Man page |
| qtl2-internal | Man page |
| qtl2-package | Man page |
| qtl2_temp_dir | Source code |
| qtl2version | Man page Source code |
| random_int | Source code |
| rbind.calc_genoprob | Man page Source code |
| rbind.scan1 | Man page Source code |
| rbind.scan1perm | Man page Source code |
| rbind.sim_geno | Man page Source code |
| rbind.viterbi | Man page Source code |
| read_control_file | Source code |
| read_cross2 | Man page Source code |
| read_csv | Man page Source code |
| read_csv_numer | Man page Source code |
| read_header | Source code |
| read_mult_csv | Source code |
| read_pheno | Man page Source code |
| read_phenocovar | Source code |
| recode_geno | Source code |
| recode_snps | Man page Source code |
| reduce_map_gaps | Man page Source code |
| reduce_markers | Man page Source code |
| reduce_markers_onechr | Source code |
| reduce_to_index_snps | Source code |
| reorder_map_table | Source code |
| replace_ids | Man page Source code |
| replace_ids.calc_genoprob | Man page Source code |
| replace_ids.cross2 | Man page Source code |
| replace_ids.data.frame | Man page |
| replace_ids.matrix | Man page Source code |
| replace_ids.sim_geno | Man page Source code |
| replace_ids.viterbi | Man page Source code |
| rev_snp_index | Source code |
| rqtl1_chrtype | Source code |
| rqtl1_crosstype | Source code |
| rqtl_getgenonames | Source code |
| rqtl_getid | Source code |
| rqtl_getsex | Source code |
| rqtl_nind | Source code |
| rqtl_pull_map | Source code |
| rqtl_reviseXdata | Source code |
| scale_kinship | Man page Source code |
| scan1 | Man page Source code |
| scan1_binary_clean | Source code |
| scan1_clean | Source code |
| scan1_pg | Source code |
| scan1_pg_clean | Source code |
| scan1blup | Man page Source code |
| scan1blup_pg | Source code |
| scan1coef | Man page Source code |
| scan1coef_names | Source code |
| scan1coef_pg | Source code |
| scan1max | Man page Source code |
| scan1max_pg | Source code |
| scan1perm | Man page Source code |
| scan1perm_covar | Source code |
| scan1perm_nocovar | Source code |
| scan1perm_pg | Source code |
| scan1perm_pg_onechr | Source code |
| scan1snps | Man page Source code |
| scan1snps_snpinfo | Source code |
| scan_binary_onechr | Source code |
| scan_binary_onechr_intcovar_highmem | Source code |
| scan_binary_onechr_intcovar_lowmem | Source code |
| scan_binary_onechr_intcovar_weighted_highmem | Source code |
| scan_binary_onechr_intcovar_weighted_lowmem | Source code |
| scan_binary_onechr_weighted | Source code |
| scan_hk_onechr | Source code |
| scan_hk_onechr_intcovar_highmem | Source code |
| scan_hk_onechr_intcovar_lowmem | Source code |
| scan_hk_onechr_intcovar_weighted_highmem | Source code |
| scan_hk_onechr_intcovar_weighted_lowmem | Source code |
| scan_hk_onechr_nocovar | Source code |
| scan_hk_onechr_weighted | Source code |
| scan_pg_onechr | Source code |
| scan_pg_onechr_intcovar_highmem | Source code |
| scan_pg_onechr_intcovar_lowmem | Source code |
| scanblup | Source code |
| scancoefSE_binary_addcovar | Source code |
| scancoefSE_binary_intcovar | Source code |
| scancoefSE_hk_addcovar | Source code |
| scancoefSE_hk_intcovar | Source code |
| scancoefSE_pg_addcovar | Source code |
| scancoefSE_pg_intcovar | Source code |
| scancoef_binary_addcovar | Source code |
| scancoef_binary_intcovar | Source code |
| scancoef_hk_addcovar | Source code |
| scancoef_hk_intcovar | Source code |
| scancoef_pg_addcovar | Source code |
| scancoef_pg_intcovar | Source code |
| sdp2char | Man page Source code |
| setup_cluster | Source code |
| sim_geno | Man page Source code |
| sim_geno2 | Source code |
| smooth_gmap | Man page Source code |
| snpinfo_to_map | Source code |
| snpprob_from_cross | Source code |
| split_geno | Source code |
| split_map | Source code |
| sqrt_weights | Source code |
| stop_if_no_file | Source code |
| subset.calc_genoprob | Man page Source code |
| subset.cross2 | Man page Source code |
| subset.scan1 | Man page |
| subset.sim_geno | Man page Source code |
| subset.viterbi | Man page Source code |
| subset_chr | Source code |
| subset_ind | Source code |
| subset_kinship | Source code |
| subset_scan1 | Man page Source code |
| subtractlog | Source code |
| summary.compare_geno | Man page |
| summary.cross2 | Man page Source code |
| summary.scan1perm | Man page Source code |
| summary_compare_geno | Man page Source code |
| summary_scan1perm | Man page Source code |
| swap_colname | Source code |
| test_check_geno | Source code |
| test_emit | Source code |
| test_emitmatrix | Source code |
| test_founder_geno_values | Source code |
| test_init | Source code |
| test_initvector | Source code |
| test_ngen | Source code |
| test_nrec | Source code |
| test_possible_gen | Source code |
| test_step | Source code |
| test_stepmatrix | Source code |
| top_snps | Man page Source code |
| tot_mar | Man page Source code |
| unsmooth_gmap | Man page Source code |
| viridis_qtl2 | Source code |
| viterbi | Man page Source code |
| viterbi2 | Source code |
| weight_array | Source code |
| weight_kinship | Source code |
| weight_matrix | Source code |
| weight_vector | Source code |
| weighted_3darray | Source code |
| weighted_matrix | Source code |
| write_control_file | Man page Source code |
| xpos_scan1 | Man page Source code |
| zip_datafiles | Man page Source code |
