| add_pmap | Add physical map contents to tibble |
| boot_pvl | Perform bootstrap sampling and calculate test statistic for... |
| calc_Bhat | Calculate estimated allele effects, B matrix |
| calc_covs | Calculate Vg and Ve from d-variate phenotype and kinship |
| calc_invsqrt_mat | Calculate matrix inverse square root for a covariance matrix |
| calc_lrt_tib | Calculate a likelihood ratio test statistic from the output... |
| calc_profile_lods | Calculate profile lods for all traits |
| calc_Sigma | Calculate the phenotypes covariance matrix Sigma |
| calc_sqrt_mat | Calculate matrix square root for a covariance matrix |
| check_identical | Check whether a vector, x, has all its entries equal to its... |
| check_missingness | Check for missingness in phenotypes or covariates |
| convert_to_scan1_output | Convert 'scan_multi_oneqtl' output of 'qtl2::scan1' output |
| find_pleio_peak_tib | Find the marker index corresponding to the peak of the... |
| fit1_pvl | Fit a model for a specified d-tuple of markers |
| get_effects | Extract founder allele effects at a single marker from output... |
| make_id2keep | Identify shared subject ids among all inputs: covariates,... |
| pipe | Pipe operator |
| plot_pvl | Plot tidied results of a pvl scan |
| prep_mytab | Prepare mytab object for use within scan_pvl R code |
| prep_X_list | Create a list of component X matrices for input to... |
| process_inputs | Process inputs to scan functions |
| qtl2pleio | qtl2pleio. |
| rcpp_calc_Bhat | Estimate allele effects matrix, B hat, with Rcpp functions |
| rcpp_calc_Bhat2 | Estimate allele effects matrix, B hat, with Rcpp functions |
| rcpp_log_dmvnorm2 | Calculate log likelihood for a multivariate normal |
| scan_multi_onechr | Perform multivariate, one-QTL model fitting for markers on... |
| scan_multi_oneqtl | Perform multivariate, one-QTL model fitting for markers on... |
| scan_multi_oneqtl_perm | Permute the phenotypes matrix and then scan the genome.... |
| scan_pvl | Perform model fitting for all ordered pairs of markers in a... |
| sim1 | Simulate a single multivariate data set consisting of n... |
| subset_input | Subset an input object - allele probabilities array or... |
| subset_kinship | Subset a kinship matrix to include only those subjects... |
