R/NBGOF-package.R

In gu-mi/NBGOF: Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data

################################################################################
## Copyright (C) 2014 Gu Mi <mig@stat.oregonstate.edu>
## 
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later version.
## 
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.
## 
## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
## 02110-1301, USA
################################################################################

# Package Documentation
# 
# Author: Gu Mi
################################################################################

#' @title Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of 
#' RNA Sequencing Data
#' 
#' @description An R package for implementing goodness-of-fit tests for negative binomial (NB)
#' distributions and NB dispersion models, with applications in RNA-Seq data analysis.
#' 
#' @details 
#' This package can be used to test the goodness-of-fit of NB2, NBP or Poisson regression
#' models. It can also be used to test the goodness-of-fit for a variety of negative binomial
#' dispersion models in popular R/Bioconductor packages, including
#' \itemize{
#' \item NBP dispersion model in the \code{NBPSeq} package (\code{NBP})
#' \item NBQ dispersion model in the \code{NBPSeq} package (\code{NBQ})
#' \item NB common dispersion model in the \code{\link{edgeR}} package (\code{Common})
#' \item NB genewise dispersion model in the \code{\link{edgeR}} package (\code{Genewise})
#' \item NB trended (non-parametric) dispersion model in the \code{\link{edgeR}} package
#' (\code{Trended})
#' \item NB tagwise-common dispersion model in the \code{\link{edgeR}} package 
#' (\code{Tagwise-Common})
#' \item NB tagwise-trended dispersion model in the \code{\link{edgeR}} package 
#' (\code{Tagwise-Trend})
#' }
#' 
#' @name NBGOF-package
#' @aliases NBGOF-package NBGOF
#' @docType package
#' @import NBPSeq edgeR numDeriv MASS parallel foreach ggplot2 grid
#' @useDynLib NBGOF Cdqrls
#' 
#' @author Gu Mi <neo.migu@@gmail.com>, Yanming Di, Daniel Schafer
#' 
#' Maintainer: Gu Mi <https://github.com/gu-mi>
#' 
#' @seealso See \code{\link{nb.gof.v}} and \code{\link{nb.gof.m}} for examples on simulated
#' datasets. See \code{\link{earthquake}} and \code{\link{arab}} for real data examples.
#' 
#' @references 
#' Mi, G, Di, Y, & Schafer, DW (2015). Goodness-of-Fit Tests and Model Diagnostics for 
#' Negative Binomial Regression of RNA Sequencing Data. \emph{PLOS ONE}, 10 (3).
#' 
#' Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): "The NBP Negative Binomial
#' Model for Assessing Differential Gene Expression from RNA-Seq", \emph{Statistical 
#' Applications in Genetics and Molecular Biology}, 10 (1).
#' 
#' McCarthy DJ, Chen Y and Smyth GK (2012). Differential expression analysis of multifactor 
#' RNA-Seq experiments with respect to biological variation. \emph{Nucleic Acids Research} 
#' 40, 4288-4297.
#' 
#' Cox, DR, and Reid, N (1987). Parameter orthogonality and approximate conditional inference.
#' \emph{Journal of the Royal Statistical Society Series B} 49, 1-39.
#' 
#' See \url{https://github.com/gu-mi/NBGOF/wiki/} for more details.
#'
#' @keywords package 
#' 
NULL

.onLoad <- function(libname, pkgname){
  
  # suppress loading package messages
  suppressMessages(library(doMC))
  suppressMessages(library(foreach))
  suppressMessages(library(iterators))
  suppressMessages(library(parallel))
  suppressMessages(library(ggplot2))
  suppressMessages(library(grid))
  #
  # startup message of our own package
#   packageStartupMessage("Loading NBGOF ...", appendLF = FALSE)
#   Sys.sleep(1)
#   packageStartupMessage(" done")
  message("\n For updates of the NBGOF package, please visit https://github.com/gu-mi/NBGOF \n")
}