Implementation of Several Phenotype-Based Family Genetic Risk Scores

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Documentation for package ‘LTFGRS’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.