API for rqtl/qtl2scan
Genome Scans for QTL Experiments
| Global functions | |
|---|---|
| .Xgenoprob_to_snpprob | Source code |
| .alleleprob_to_snpprob | Source code |
| .bayes_int_plain | Source code |
| .calc_sdp | Source code |
| .find_peaks | Source code |
| .find_peaks_and_bayesint | Source code |
| .find_peaks_and_lodint | Source code |
| .genoprob_to_snpprob | Source code |
| .invert_sdp | Source code |
| .lod_int_plain | Source code |
| .pick_marker_subset | Source code |
| Rcpp_calcLL | 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` | Source code |
| align_scan1_map | Source code |
| batch_cols | Man page Source code |
| batch_vec | 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_fitted_linreg_eigenchol | Source code |
| calc_fitted_linreg_eigenqr | Source code |
| calc_hsq_clean | 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_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.scan1 | Man page Source code |
| cbind.scan1perm | Man page Source code |
| cbind_expand | Source code |
| check4names | Source code |
| check_binary_pheno | Source code |
| check_extra_dots | Source code |
| check_kinship | Source code |
| check_kinship_onechr | Source code |
| chr_lengths | Man page Source code |
| cluster_lapply | Source code |
| collapse_chr_lengths_to_AX | Source code |
| colnames4attr | 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_xcovar | Source code |
| est_herit | Man page Source code |
| expand_genoprobs_intcovar | Source code |
| expand_interval_to_markers | Source code |
| find_intervals | Source code |
| find_lin_indep_cols | 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 |
| 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 |
| gen_strat_perm | Source code |
| genocol_to_snpcol | 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 |
| grab_dots | Source code |
| hsq_dimnames | Source code |
| index_batches_by_omits | Source code |
| index_snps | Man page Source code |
| interp_map | Man page Source code |
| interpolate_map | Source code |
| invert_sdp | Man page Source code |
| is_cluster | Source code |
| is_kinship_decomposed | Source code |
| is_kinship_list | Source code |
| is_same | Source code |
| isnt_karl | Source code |
| lod_int | Man page Source code |
| map2chr | Source code |
| map2markernames | Source code |
| map2pos | Source code |
| mat2strata | Man page Source code |
| matrix_x_3darray | Source code |
| matrix_x_matrix | Source code |
| matrix_x_vector | Source code |
| max.scan1 | Man page Source code |
| max_scan1 | Man page Source code |
| maxlod | Man page Source code |
| n_cores | 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 |
| pick_marker_subset | Man page Source code |
| print.summary.scan1perm | Man page Source code |
| qtl2scan | Man page |
| qtl2scan-package | Man page |
| random_int | Source code |
| rbind.scan1 | Man page Source code |
| rbind.scan1perm | Man page Source code |
| rev_snp_index | 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 |
| 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 |
| setup_cluster | Source code |
| snpinfo_to_map | Source code |
| sqrt_weights | Source code |
| subset.calc_genoprob | Source code |
| subset.scan1 | Man page |
| subset_chr | Source code |
| subset_ind | Source code |
| subset_kinship | Source code |
| subset_scan1 | Man page Source code |
| summary.scan1perm | Man page Source code |
| summary_scan1perm | Man page Source code |
| top_snps | Man page Source code |
| weighted_3darray | Source code |
| weighted_matrix | Source code |
