R: Implementation of Several Phenotype-Based Family Genetic Risk Scores

# Implementation of Several Phenotype-Based Family Genetic Risk Scores

## Documentation for package ‘LTFGRS’ version 1.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

attach_attributes | Attach attributes to a family graphs
censor_family_onsets | Censor onset times in a family based on a proband's end of follow-up.
construct_covmat | Constructing a covariance matrix for a variable number of phenotypes
construct_covmat_multi | Constructing a covariance matrix for multiple phenotypes
construct_covmat_single | Constructing a covariance matrix for a single phenotype
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
correct_positive_definite | Positive definite matrices
estimate_gen_liability_ltfh | Estimate genetic liability similar to LT-FH
estimate_liability | Estimating the genetic or full liability for a variable number of phenotypes
estimate_liability_multi | Estimating the genetic or full liability for multiple phenotypes
estimate_liability_single | Estimating the genetic or full liability
extract_estimation_info_graph | Title Internal Function used to extact input needed from graph input for liability estimation
extract_estimation_info_tbl | Title Internal Function used to extact input needed for liability estimation
familywise_attach_attributes | Wrapper to attach attributes to family graphs
familywise_censoring | Censor Family Onsets for Multiple Families
fixSexCoding | Fixing sex coding in trio info
get_all_combs | construct all combinations of input vector
get_covmat | Construct kinship matrix from graph
get_family_graphs | Automatically identify family members of degree n
get_onset_time | Calculate age of diagnosis, age at end of follow up, and status
get_relatedness | Relatedness between a pair of family members
Gibbs_estimator | Wrapper around the Gibbs Sampler that returns formatted liability estimates for the proband
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
graph_to_trio | Convert from igraph to trio information
kendler | Title Kendler's FGRS
kendler_family_calculations | Title Helper function for Kendler's FGRS
PA_algorithm | Title Pearson-Aitken algorithm to calculate mean values in truncated multivariate normal distributions
prepare_graph | Construct graph from register information
prepare_thresholds | Calculate (personalised) thresholds based on CIPs.
rtmvnorm.gibbs | Gibbs Sampler for the truncated multivariate normal distribution
simulate_under_LTM | Simulate under the liability threshold model.
simulate_under_LTM_multi | Simulate under the liability threshold model (multiple phenotypes).
simulate_under_LTM_single | Simulate under the liability threshold model (single phenotype).
tnorm_mean | Title: Calculate the mean of the truncated normal distribution
tnorm_mixture_conditional | Title: Calculates mean and variance of mixture of two truncated normal distributions
tnorm_var | Title: Calculate the variance of the truncated normal distribution
truncated_normal_cdf | CDF for truncated normal distribution.