Implementation of LT-FH++
Compute and Label Pairwise Relationships Across Multiple Family Graphs
Convert age to threshold
Convert cumulative incidence rate to age
Attempts to convert the list entry input format to a long format
Wrapper to attach attributes to family graphs
Fixing sex coding in trio info
construct all combinations of input vector
Automatically identify family members of degree n
Compute Generational Distances and Kinship Coefficients from a Family ...
Construct kinship matrix from graph
Relatedness between a pair of family members
Convert age to cumulative incidence rate
Attach attributes to a family graphs
Constructing a covariance matrix for multiple phenotypes
Constructing a covariance matrix for a single phenotype
Constructing a covariance matrix for a variable number of phenotypes
Convert liability to age of onset
Convert the heritability on the observed scale to that on the liabilit...
Positive definite matrices
Estimate genetic liability similar to LT-FH
Estimating the genetic or full liability for multiple phenotypes
Estimating the genetic or full liability
Estimating the genetic or full liability for a variable number of phen...
Constructing covariance matrix from local family graph for multi trait...
Constructing covariance matrix from local family graph
Convert from igraph to trio information
Label Pairwise Relationships Based on Generational Distance and Kinshi...
LTFHPlus: Implementation of LT-FH++
Construct graph from register information
Prepares input for estimate_liability
Plot the (Average) Number of Relatives per Proband by Relationship Typ...
Gibbs Sampler for the truncated multivariate normal distribution
Simulate under the liability threshold model (multiple phenotypes).
Simulate under the liability threshold model (single phenotype).
Simulate under the liability threshold model.
CDF for truncated normal distribution.
Implementation of LT-FH++, an extension of the liability threshold family history (LT-FH) model. LT-FH++ uses a Gibbs sampler for sampling from the truncated multivariate normal distribution and allows for flexible family structures. LT-FH++ was first described in Pedersen, Emil M., et al. (2022) <doi:10.1016/j.ajhg.2022.01.009> as an extension to LT-FH with more flexible family structures, and again as the age-dependent liability threshold (ADuLT) model Pedersen, Emil M., et al. (2023) <https://www.nature.com/articles/s41467-023-41210-z> as an alternative to traditional time-to-event genome-wide association studies, where family history was not considered.
Useful links