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add_pmap()
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Add physical map contents to tibble |
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boot_pvl()
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Perform bootstrap sampling and calculate test statistic for each bootstrap sample |
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calc_Bhat()
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Calculate estimated allele effects, B matrix |
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calc_Sigma()
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Calculate the phenotypes covariance matrix Sigma |
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calc_covs()
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Calculate Vg and Ve from d-variate phenotype and kinship |
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calc_invsqrt_mat()
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Calculate matrix inverse square root for a covariance matrix |
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calc_lrt_tib()
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Calculate a likelihood ratio test statistic from the output of scan_pvl() |
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calc_profile_lods()
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Calculate profile lods for all traits |
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calc_sqrt_mat()
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Calculate matrix square root for a covariance matrix |
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check_identical()
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Check whether a vector, x, has all its entries equal to its first entry |
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check_missingness()
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Check for missingness in phenotypes or covariates |
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convert_to_scan1_output()
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Convert `scan_multi_oneqtl` output of `qtl2::scan1` output |
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find_pleio_peak_tib()
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Find the marker index corresponding to the peak of the pleiotropy trace in a tibble where the last column contains log likelihood values and the first d columns contain marker ids |
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fit1_pvl()
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Fit a model for a specified d-tuple of markers |
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get_effects()
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Extract founder allele effects at a single marker from output of qtl2::scan1coef |
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make_id2keep()
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Identify shared subject ids among all inputs: covariates, allele probabilities array, kinship, and phenotypes |
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plot_pvl()
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Plot tidied results of a pvl scan |
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prep_X_list()
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Create a list of component X matrices for input to stagger_mats, to ultimately create design matrix |
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prep_mytab()
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Prepare mytab object for use within scan_pvl R code |
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process_inputs()
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Process inputs to scan functions |
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qtl2pleio
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qtl2pleio. |
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rcpp_calc_Bhat()
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Estimate allele effects matrix, B hat, with Rcpp functions |
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rcpp_calc_Bhat2()
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Estimate allele effects matrix, B hat, with Rcpp functions |
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rcpp_log_dmvnorm2()
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Calculate log likelihood for a multivariate normal |
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scan_multi_onechr()
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Perform multivariate, one-QTL model fitting for markers on one chromosome |
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scan_multi_oneqtl()
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Perform multivariate, one-QTL model fitting for markers on all chromosomes |
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scan_multi_oneqtl_perm()
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Permute the phenotypes matrix and then scan the genome. Record the genomewide greatest LOD score for each permuted data set. |
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scan_pvl()
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Perform model fitting for all ordered pairs of markers in a genomic region of interest |
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sim1()
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Simulate a single multivariate data set consisting of n subjects and d phenotypes for each |
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subset_input()
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Subset an input object - allele probabilities array or phenotypes matrix or covariates matrix. Kinship has its own subset function |
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subset_kinship()
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Subset a kinship matrix to include only those subjects present in all inputs |