R/LBL.R

In mxw010/LBL: Logistic and Quantitative Bayesian Lasso for identifying genetic association between common diseases and rare haplotypes

#' LBL: Logistic Bayesian Lasso for Detecting Rare (or Common) Haplotype Association
#'
#' LBL uses the Bayesian LASSO framework to detect association between
#' a phenotype and haplotypes given the (unphased) genotypes of individuals.
#'
#' LBL uses Bayesian Lasso to detect rare haplotypes that are associated with common diseases. 
#' The current implementation considers dichotomous traits. A future release will include quantitative and survival traits.
#' LBL is capable of handling different study designs: this version of the software is capable of handling independent cases and controls, case-parent trios and a mixture of both (provided
#' that the family data is independent of the case-control data). 
#'
#' A function from the hapassoc package is first used to acquire all compatible haplotypes. 
#' The posterior samples are then obtained via Markov Chain Monte Carlo (MCMC)
#' algorithm and inference on the parameters of interest can be carried out
#' (Bayes Factor, Credible Interval, etc.) based on these posterior samples.
#'
#' @section Functions:
#' \code{\link{LBL}}:  MCMC algorithm to obtain posterior samples for independent case-control data.
#' \code{\link{famLBL}}:  MCMC algorithm to obtain posterior samples for case-parent trio data.
#' \code{\link{cLBL}}:  MCMC algorithm to obtain posterior samples for combined data.
#'
#' \code{\link{LBL_summary}} provides model summary (in the form of list) based on posterior samples.
#' \code{\link{print_LBL_summary}} prints model summary in a user-friendly format from the list result of \code{\link{LBL_summary}}.
#'
#' 
#' @author Swati Biswas, Meng Wang, Xiaofei Zhou, Han Zhang, Shuang Xia, Yuan Zhang, and Shili Lin <shili@@stat.osu.edu>
#' 
#' @references
#'
#' Biswas S. and Lin S. (2012). Logistic Bayesian LASSO for identifying
#'   association with rare haplotypes and application to age-related macular
#'   degeneration. \emph{Biometrics}, 68(2): 587-97.
#'
#' Wang, M. and Lin, S. (2014). FamLBL: detecting rare haplotype disease association
#'   based on common SNPs using case-parent triads. \emph{Bioinformatics}, 30(18), 2611-2618.
#'
#' Zhou, X., Wang, M., and Lin, S. (2019). cLBL: Combined logistic Bayesian LASSO for 
#' detecting rare associated haplotypes using independent case, control and family trio 
#' data. \emph{Manuscript}.
#' @docType package
#' @name LBL-package
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