Man pages for eriqande/fullsniplings
Full sibling reconstruction from SNP data
| alle_freqs | counts alleles from a geno_counts matrix |
| ave_err_commission_and_ommission | computes the average number of non-sibs in inferred sibships |
| C_full_sibling_pair_gfreqs | compute the genotype probs of a pair of full siblings with... |
| count_genos | counts up genotypes from a snp_indicators array |
| find_high_logl_sib_pairs | for each individual, find the other individuals with a... |
| full_sibling_pair_gfreqs | returns genotype probabilities of a pair of full siblings |
| full_sib_mcmc_initialize | initilize all the variables to do a full sibling analysis... |
| fullsniplings | Full-sibling inference from biallelic markers (like SNPs) |
| geno_post_c | compute the posterior of Inds genotype given the genotype... |
| geno_posterior | given some genotype likelihoods and a prior, compute the... |
| geno_qty_array | S3 class for arrays holding probabilities and likelihoods of... |
| genos_to_indicators | Take an L x N matrix of SNP genos and return a 3 x L x N... |
| get_indiv_geno_lik | given genotyping error and observed genotypes, return an... |
| get_snp_genos | takes a data frame of SNP alleles and converts them to a... |
| gfreqs_from_afreqs | creates a vector of genotypes likelihoods from the allele... |
| gibbs_update_one_indiv_in_place | does a gibbs update of the full sibling group of individual... |
| gqa_natural | return a geno_qty_array in its natural representation with... |
| greedy_partition | Uses the estimated posteriors for each sibgroup to come up... |
| hashable_sibships | Returns a vector of strings naming the current sibships |
| high_logl_pairs | return the high-sib-pair-logl indivs for each indiv |
| initialize_sib_list_to_singletons | initialize the list of full siblings to a bunch of singletons |
| kid_prongs_times_ind_likelihoods | Computes the posterior predictive likelihoods that an... |
| lik_array_from_simple_geno_err | makes L 3x3 tables of genotype likelihoods |
| make_IFS_from_FSL | create the "individuals full sibships" vector from the... |
| make_KidProngs_from_FSL_and_PMMFS | create a KidProngs matrix (matrix of posterior predictives... |
| make_LMMFS_from_FSL_and_LMMI | create the "Likelihood Matrix of Marriages given Full... |
| make_PMMFS_from_FSL_and_LMMFS | create a "Posterior Matrix of Marriages given Full Siblings"... |
| multi_kid_marriage_likelihoods | compute the marriage node likelihoods given offspring... |
| NamizeSibs | adds the names of the members of the sibset if available |
| ordered_fsl | Orders the Full Sibling List (FSL) by size and orders the... |
| per_kid_marriage_likelihoods | Compute the likelihood of the genotypes of a marriage given... |
| possible_sibgroups | return a vector of indices of sibships that include at least... |
| prep_all_variables | a function to prep all the variables up through the marriage... |
| print.geno_qty_array | a method for printing objects inheriting from class... |
| pseudo_prior | compute the pseudo-prior for individual and individual pulled... |
| run_mcmc | Run the MCMC for full sibling inference |
| sib_result_plot | plot posterior bars and compare to correct or incorrect |
| simulate_sib_pair_logls | simulate pairs of full sibs and pairs of unrelateds and... |
| SlurpSibships | Slurps a colony inferred sibship file into a list |
| sort_visited_sibgroups | sorts the visited sibgroups on the basis of posterior and... |
| table_sibsizes | this function tables the sibship sizes |
| trans_probs | returns a matrix of the 27 transmission probs between a pair... |
| unrelated_pair_gfreqs | creates a matrix of genotype probabilities for two unrelated... |
| update_marriage_likelihoods_in_place | Update one row of a marriage likelihood matrix IN PLACE! |
| update_marriage_node_kid_prongs_in_place | update marriage node kid prongs IN PLACE |
| update_marriage_posteriors_in_place | Calculate/update one row of a marriage Posterior matrix IN... |
