Package index • LTFHPlus

Estimating (Genetic) Liability

Functions used to estimate the genetic liability in a range of different setups with and without family history and prevalence information.

estimate_liability(): Estimating the genetic or full liability for a variable number of phenotypes

Helper functions

Collection of functions used as examples of how to include additional information.

prepare_LTFHPlus_input(): Prepares input for estimate_liability

prepare_graph(): Construct graph from register information

graph_to_trio(): Convert from igraph to trio information

convert_age_to_cir(): Convert age to cumulative incidence rate

convert_age_to_thresh(): Convert age to threshold

convert_cir_to_age(): Convert cumulative incidence rate to age

convert_format(): Attempts to convert the list entry input format to a long format

convert_liability_to_aoo(): Convert liability to age of onset

convert_observed_to_liability_scale(): Convert the heritability on the observed scale to that on the liability scale

simulate_under_LTM(): Simulate under the liability threshold model.

truncated_normal_cdf(): CDF for truncated normal distribution.

Auxiliary functions

Functions used to define covariance matrices.

rtmvnorm.gibbs(): Gibbs Sampler for the truncated multivariate normal distribution

get_kinship(): Construct kinship matrix from graph

get_relatedness(): Relatedness between a pair of family members

construct_covmat_single(): Constructing a covariance matrix for a single phenotype

construct_covmat_multi(): Constructing a covariance matrix for multiple phenotypes

construct_covmat(): Constructing a covariance matrix for a variable number of phenotypes

correct_positive_definite(): Positive definite matrices

graph_based_covariance_construction(): Constructing covariance matrix from local family graph

graph_based_covariance_construction_multi(): Constructing covariance matrix from local family graph for multi trait analysis

Legacy & internal functions

functions that are not currently being used, but kept for compatabilitity and internal functions used by the package.

get_all_combs(): construct all combinations of input vector

estimate_gen_liability_ltfh(): Estimate genetic liability similar to LT-FH

estimate_liability_multi(): Estimating the genetic or full liability for multiple phenotypes

estimate_liability_single(): Estimating the genetic or full liability

simulate_under_LTM_multi(): Simulate under the liability threshold model (multiple phenotypes).

simulate_under_LTM_single(): Simulate under the liability threshold model (single phenotype).

fixSexCoding(): Fixing sex coding in trio info