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analyse_mixture_result()
|
Analyse mixture results |
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analyse_mixture_results()
|
Analyse mixture results in a vectorised fashion |
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as_tbl_graph(<malan_pedigreelist>)
|
Get tidy graph object |
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brothers_matching()
|
Number of brothers with matching haplotype |
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build_haplotype_hashmap()
|
Build hashmap of haplotype to individuals |
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build_pedigrees()
|
Build pedigrees from (individuals in) a population. |
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calc_autosomal_genotype_conditional_cumdist()
|
Calculate conditional genotype cumulative probabilities with theta |
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calc_autosomal_genotype_probs()
|
Calculate genotype probabilities with theta |
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construct_M()
|
Construct M matrix |
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count_brothers()
|
Number of brothers |
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count_haplotype_near_matches_individuals()
|
Count near haplotype matches in list of individuals |
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count_haplotype_occurrences_individuals()
|
Count haplotypes occurrences in list of individuals |
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count_haplotype_occurrences_pedigree()
|
Count haplotypes occurrences in pedigree |
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count_uncles()
|
Number of uncles |
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delete_haplotypeids_hashmap()
|
Delete haplotype hashmap |
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estimate_autotheta_1subpop_genotypes()
|
Estimate autosomal theta from genotypes |
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estimate_autotheta_1subpop_individuals()
|
Estimate autosomal theta from individuals |
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estimate_autotheta_subpops_genotypes()
|
Estimate autosomal F, theta, and f from subpopulations of genotypes |
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estimate_autotheta_subpops_individuals()
|
Estimate autosomal F, theta, and f from subpopulations of individuals |
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estimate_autotheta_subpops_pids()
|
Estimate autosomal F, theta, and f from subpopulations of individual ids |
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estimate_autotheta_subpops_unweighted_genotypes()
|
Unweighted estimate of autosomal theta from subpopulations of genotypes |
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estimate_autotheta_subpops_unweighted_pids()
|
Unweighted estimate of autosomal theta from subpopulations of individual ids |
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father_matches()
|
Father matches |
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from_igraph()
|
Convert igraph to population |
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from_igraph_rcpp()
|
Generate paternal brothers population |
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generate_get_founder_haplotype_db()
|
Generate a function to simulate pedigree founder haplotype based on a haplotype databasep |
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generate_get_founder_haplotype_ladder()
|
Generate a function to simulate pedigree founder haplotype based on ladder information |
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get_allele_counts_genotypes()
|
Get autosomal allele counts from subpopulations of genotypes |
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get_allele_counts_pids()
|
Get autosomal allele counts from subpopulations given by pids |
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get_brothers()
|
Get brothers |
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get_children()
|
Get children |
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get_cousins()
|
Get cousins |
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get_family_info()
|
Get individual's family information |
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get_father()
|
Get father |
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get_generation()
|
Get individual's generation number |
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get_haplotype()
|
Get haplotype from an individual |
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get_haplotypes_in_pedigree()
|
Get haplotypes in pedigree |
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get_haplotypes_individuals()
|
Get haplotype matrix from list of individuals |
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get_haplotypes_pids()
|
Get haplotypes from a vector of pids. |
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get_individual()
|
Get individual by pid |
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get_individuals()
|
Get all individuals in population |
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get_matching_pids_from_hashmap()
|
Get individuals with a certain haplotype id by hashmap lookup |
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get_nodes_edges()
|
Get nodes and edges |
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get_pedigree_as_graph()
|
Get pedigree information as graph (mainly intended for plotting) |
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get_pedigree_from_individual()
|
Get pedigree from individual |
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get_pedigree_id()
|
Get pedigree id |
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get_pedigree_id_from_pid()
|
Get pedigree ids from pids |
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get_pedigrees_tidy()
|
Get pedigrees information in tidy format |
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get_pid()
|
Get pid from individual |
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get_pids_in_pedigree()
|
Get pids in pedigree |
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get_uncles()
|
Get uncles |
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get_zero_haplotype_generator()
|
Generate a function to generate the zero haplotype |
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grandfather_matches()
|
Grandfather matches |
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haplotype_matches_individuals()
|
Get individuals matching from list of individuals |
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haplotype_partially_matches_individuals()
|
Get individuals partially matching from list of individuals |
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haplotypes_to_hashes()
|
Convert haplotypes to hashes (integers) |
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infer_generations()
|
Infer generation numbers from pedigrees |
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load_individuals()
|
Construct a population from data |
|
malan-package
|
MAle Lineage ANalysis |
|
meioses_generation_distribution()
|
Meiotic distribution |
|
meiotic_dist()
|
Meiotic distance between two individuals |
|
mixture_info_by_individuals_2pers()
|
Mixture information about 2 persons' mixture of donor1 and donor2. |
|
mixture_info_by_individuals_3pers()
|
Mixture information about 3 persons' mixture of donor1, donor2 and donor3. |
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mixture_info_by_individuals_4pers()
|
Mixture information about 4 persons' mixture of donor1, donor2, donor3 and donor4. |
|
mixture_info_by_individuals_5pers()
|
Mixture information about 5 persons' mixture of donor1, donor2, donor3, donor4 and donor5. |
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pedigree_as_igraph()
|
Convert pedigree to igraph |
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pedigree_haplotype_matches_in_pedigree_meiosis_L1_dists()
|
Information about matching individuals |
|
pedigree_haplotype_near_matches_meiosis()
|
Information about almost matching individuals |
|
pedigree_size()
|
Get pedigree size |
|
pedigree_size_generation()
|
Size of pedigree |
|
pedigrees_all_populate_autosomal()
|
Populate 1-locus autosomal DNA profile in pedigrees with single-step mutation model. |
|
pedigrees_all_populate_haplotypes()
|
Populate haplotypes in pedigrees (0-founder/unbounded). |
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pedigrees_all_populate_haplotypes_custom_founders()
|
Populate haplotypes in pedigrees (custom founder/unbounded). |
|
pedigrees_all_populate_haplotypes_ladder_bounded()
|
Populate haplotypes in pedigrees (custom founder/bounded). |
|
pedigrees_count()
|
Get number of pedigrees |
|
pedigrees_table()
|
Get distribution of pedigree sizes |
|
plot(<malan_pedigree>)
|
Plot pedigree |
|
plot(<malan_pedigreelist>)
|
Plot pedigree list |
|
population_populate_autosomal_infinite_alleles()
|
Populate 1-locus autosomal DNA profile in pedigrees with infinite alleles mutation model. |
|
population_size_generation()
|
Size of population |
|
print(<malan_pedigree>)
|
Print pedigree |
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print(<malan_pedigreelist>)
|
Print pedigree list |
|
print(<malan_population>)
|
Print population |
|
print(<malan_population_abort>)
|
Print malan_population_abort |
|
print_individual()
|
Print individual |
|
relationship_allele_diff_dist()
|
Calculate distribution of allele difference |
|
relationship_allele_diff_dist_sym()
|
Calculate distribution of allele difference for symmetric mutation rates |
|
sample_autosomal_genotype()
|
Sample genotype with theta |
|
sample_geneology()
|
Simulate a geneology with constant population size. |
|
sample_geneology_varying_size()
|
Simulate a geneology with varying population size. |
|
split_by_haplotypes()
|
Split pids by haplotype |
|
`[[`(<malan_pedigreelist>)
|
Get pedigree from pedigree list |
|
`[[`(<malan_population>)
|
Get individual from population by pid |
|
test_create_population()
|
Generate test population |
|
ystr_kits
|
Kit information about Y-STR markers |
|
ystr_markers
|
Mutational information about Y-STR markers |