MAle Lineage ANalysis

Documentation for package ‘malan’ version 1.0.3

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MAle Lineage ANalysis

-- A --

analyse_mixture_result	Analyse mixture results
analyse_mixture_results	Analyse mixture results in a vectorised fashion
as_tbl_graph.malan_pedigreelist	Get tidy graph object

-- B --

brothers_matching	Number of brothers with matching haplotype
build_haplotype_hashmap	Build hashmap of haplotype to individuals
build_pedigrees	Build pedigrees from (individuals in) a population.

-- C --

calc_autosomal_genotype_conditional_cumdist	Calculate conditional genotype cumulative probabilities with theta
calc_autosomal_genotype_probs	Calculate genotype probabilities with theta
construct_M	Construct M matrix
count_brothers	Number of brothers
count_haplotype_near_matches_individuals	Count near haplotype matches in list of individuals
count_haplotype_occurrences_individuals	Count haplotypes occurrences in list of individuals
count_haplotype_occurrences_pedigree	Count haplotypes occurrences in pedigree
count_uncles	Number of uncles

-- D --

delete_haplotypeids_hashmap

Delete haplotype hashmap

-- E --

estimate_autotheta_1subpop_genotypes	Estimate autosomal theta from genotypes
estimate_autotheta_1subpop_individuals	Estimate autosomal theta from individuals
estimate_autotheta_subpops_genotypes	Estimate autosomal F, theta, and f from subpopulations of genotypes
estimate_autotheta_subpops_individuals	Estimate autosomal F, theta, and f from subpopulations of individuals
estimate_autotheta_subpops_pids	Estimate autosomal F, theta, and f from subpopulations of individual ids
estimate_autotheta_subpops_unweighted_genotypes	Unweighted estimate of autosomal theta from subpopulations of genotypes
estimate_autotheta_subpops_unweighted_pids	Unweighted estimate of autosomal theta from subpopulations of individual ids

-- F --

father_matches	Father matches
from_igraph	Convert igraph to population
from_igraph_rcpp	Generate paternal brothers population

-- G --

generate_get_founder_haplotype_db	Generate a function to simulate pedigree founder haplotype based on a haplotype databasep
generate_get_founder_haplotype_ladder	Generate a function to simulate pedigree founder haplotype based on ladder information
get_allele_counts_genotypes	Get autosomal allele counts from subpopulations of genotypes
get_allele_counts_pids	Get autosomal allele counts from subpopulations given by pids
get_brothers	Get brothers
get_children	Get children
get_cousins	Get cousins
get_family_info	Get individual's family information
get_father	Get father
get_generation	Get individual's generation number
get_haplotype	Get haplotype from an individual
get_haplotypes_individuals	Get haplotype matrix from list of individuals
get_haplotypes_in_pedigree	Get haplotypes in pedigree
get_haplotypes_pids	Get haplotypes from a vector of pids.
get_individual	Get individual by pid
get_individuals	Get all individuals in population
get_matching_pids_from_hashmap	Get individuals with a certain haplotype id by hashmap lookup
get_nodes_edges	Get nodes and edges
get_pedigrees_tidy	Get pedigrees information in tidy format
get_pedigree_as_graph	Get pedigree information as graph (mainly intended for plotting)
get_pedigree_from_individual	Get pedigree from individual
get_pedigree_id	Get pedigree id
get_pedigree_id_from_pid	Get pedigree ids from pids
get_pid	Get pid from individual
get_pids_in_pedigree	Get pids in pedigree
get_uncles	Get uncles
get_zero_haplotype_generator	Generate a function to generate the zero haplotype
grandfather_matches	Grandfather matches

-- H --

haplotypes_to_hashes	Convert haplotypes to hashes (integers)
haplotype_matches_individuals	Get individuals matching from list of individuals
haplotype_partially_matches_individuals	Get individuals partially matching from list of individuals

-- I --

infer_generation	Infer individual's generation number
infer_generations	Infer generation numbers from pedigrees

-- L --

load_haplotypes	Load haplotypes to individuals
load_individuals	Construct a population from data

-- M --

malan	MAle Lineage ANalysis
meioses_generation_distribution	Meiotic distribution
meiotic_dist	Meiotic distance between two individuals
meiotic_dist_threshold	Meiotic distance between two individuals (with threshold)
meiotic_radius	Meiotic radius
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.
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.

-- P --

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).
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
pedigree_as_igraph	Convert pedigree to igraph
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
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
print.malan_pedigreelist	Print pedigree list
print.malan_population	Print population
print.malan_population_abort	Print 'malan_population_abort'
print_individual	Print individual

-- R --

relationship_allele_diff_dist	Calculate distribution of allele difference
relationship_allele_diff_dist_sym	Calculate distribution of allele difference for symmetric mutation rates

-- S --

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.
set_generation	Set individual's generation number
split_by_haplotypes	Split pids by haplotype

-- T --

test_create_population

Generate test population

-- Y --

ystr_kits	Kit information about Y-STR markers
ystr_markers	Mutational information about Y-STR markers

-- misc --

[[.malan_pedigreelist	Get pedigree from pedigree list
[[.malan_population	Get individual from population by pid