MAle Lineage ANalysis
Analyse mixture results
Analyse mixture results in a vectorised fashion
Get tidy graph object
Number of brothers with matching haplotype
Build hashmap of haplotype to individuals
Build pedigrees from (individuals in) a population.
Calculate conditional genotype cumulative probabilities with theta
Calculate genotype probabilities with theta
Construct M matrix
Number of brothers
Count near haplotype matches in list of individuals
Count haplotypes occurrences in list of individuals
Count haplotypes occurrences in pedigree
Number of uncles
Delete haplotype hashmap
Estimate autosomal theta from genotypes
Estimate autosomal theta from individuals
Estimate autosomal F, theta, and f from subpopulations of genotypes
Estimate autosomal F, theta, and f from subpopulations of individuals
Estimate autosomal F, theta, and f from subpopulations of individual i...
Unweighted estimate of autosomal theta from subpopulations of genotype...
Unweighted estimate of autosomal theta from subpopulations of individu...
Father matches
Convert igraph to population
Generate paternal brothers population
Generate a function to simulate pedigree founder haplotype based on a ...
Generate a function to simulate pedigree founder haplotype based on la...
Get autosomal allele counts from subpopulations of genotypes
Get autosomal allele counts from subpopulations given by pids
Get brothers
Get children
Get cousins
Get individual's family information
Get father
Get individual's generation number
Get haplotype from an individual
Get haplotypes in pedigree
Get haplotype matrix from list of individuals
Get haplotypes from a vector of pids.
Get individual by pid
Get all individuals in population
Get individuals with a certain haplotype id by hashmap lookup
Get nodes and edges
Get pedigree information as graph (mainly intended for plotting)
Get pedigree from individual
Get pedigree id
Get pedigree ids from pids
Get pedigrees information in tidy format
Get pid from individual
Get pids in pedigree
Get uncles
Generate a function to generate the zero haplotype
Grandfather matches
Get individuals matching from list of individuals
Get individuals partially matching from list of individuals
Convert haplotypes to hashes (integers)
Infer individual's generation number
Infer generation numbers from pedigrees
Load haplotypes to individuals
Construct a population from data
MAle Lineage ANalysis
Meiotic distribution
Meiotic distance between two individuals
Meiotic distance between two individuals (with threshold)
Meiotic radius
Mixture information about 2 persons' mixture of donor1 and donor2.
Mixture information about 3 persons' mixture of donor1, donor2 and don...
Mixture information about 4 persons' mixture of donor1, donor2, donor3...
Mixture information about 5 persons' mixture of donor1, donor2, donor3...
Convert pedigree to igraph
Information about matching individuals
Information about almost matching individuals
Get pedigree size
Size of pedigree
Populate 1-locus autosomal DNA profile in pedigrees with single-step m...
Populate haplotypes in pedigrees (0-founder/unbounded).
Populate haplotypes in pedigrees (custom founder/unbounded).
Populate haplotypes in pedigrees (custom founder/bounded).
Get number of pedigrees
Get distribution of pedigree sizes
Plot pedigree
Plot pedigree list
Populate 1-locus autosomal DNA profile in pedigrees with infinite alle...
Size of population
Print pedigree
Print pedigree list
Print population
Print malan_population_abort
Print individual
Calculate distribution of allele difference
Calculate distribution of allele difference for symmetric mutation rat...
Sample genotype with theta
Simulate a geneology with constant population size.
Simulate a geneology with varying population size.
Set individual's generation number
Split pids by haplotype
Get pedigree from pedigree list
Get individual from population by pid
Generate test population
MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches. Refer to papers mentioned in citation("malan") (DOI's: <doi:10.1371/journal.pgen.1007028>, <doi:10.21105/joss.00684> and <doi:10.1016/j.fsigen.2018.10.004>).