R/NBPSeq.package.R

In NBPSeq: Negative Binomial Models for RNA-Sequencing Data

##' Negative binomial (NB) two-group and regression models for
##' RNA-Sequencing data analysis. 
##'
##' See the examples of \code{\link{test.coefficient}} and
##' \code{\link{exact.nb.test}} for typical workflows of using this package.
##'
##' @name NBPSeq-package
##' @aliases NBPSeq
##' @docType package
##' @title Negative Binomial Regression Models for Statistical Analysis of RNA-Sequencing Data
##'
##' @useDynLib NBPSeq Cdqrls
##' @importFrom qvalue qvalue
##' @importFrom splines ns
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### @exportPattern "^[^\\.]" 

##' An RNA-Seq dataset from a pilot study of the defense response  of
##' Arabidopsis to infection by bacteria. We performed RNA-Seq
##' experiments on three independent biological samples from each of
##' the two treatment groups.  The matrix contains the frequencies of
##' RNA-Seq reads mapped to genes in a reference database. Rows
##' correspond to genes and columns correspond to independent
##' biological samples.
##'
##' We challenged leaves of Arabidopsis with the defense-eliciting
##' \emph{\eqn{\Delta}hrcC} mutant of \emph{Pseudomonas syringae}
##' pathovar \emph{tomato} DC3000.  We also infiltrated leaves of
##' Arabidopsis with 10mM MgCl2 as a mock inoculation. RNA was
##' isolated 7 hours after inoculation, enriched for mRNA and prepared
##' for RNA-Seq. We sequenced one replicate per channel on the
##' Illumina Genome Analyzer (http://www.illumina.com).  The length of
##' the RNA-Seq reads can vary in length depending on user preference
##' and the sequencing instrument. The dataset used here are derived
##' from a 36-cycle sequencing reaction, that we trimmed to 25mers.
##' We used an in-house computational pipeline to process, align, and
##' assign RNA-Seq reads to genes according to a reference database we
##' developed for Arabidopsis.
##'
##' @docType data
##' @name arab
##' @title Arabidopsis RNA-Seq Data Set
##' @format A 26222 by 6 matrix of RNA-Seq read frequencies.
##' @usage data(arab)
##' @references
##' Di Y, Schafer DW, Cumbie JS, and Chang JH (2011): "The NBP Negative Binomial
##' Model for Assessing Differential Gene Expression from RNA-Seq", Statistical
##' Applications in Genetics and Molecular Biology, 10 (1). 
##'
##' @author Jason S Cumbie \email{cumbiej@@onid.orst.edu}  and Jeff H Chang
##' \email{changj@@cgrb.oregonstate.edu}.
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