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\title{Top table of differentially spliced genes or exons}
\name{topSpliceDGE}
\alias{topSpliceDGE}
\description{
Top table ranking the most differentially spliced genes or exons.
}
\usage{
topSpliceDGE(lrt, test="Simes", number=10, FDR=1)
}
\arguments{
\item{lrt}{\code{DGELRT} object produced by \code{diffSpliceDGE}.}
\item{test}{character string, possible values are \code{"Simes"}, \code{"gene"} or \code{"exon"}.
\code{"exon"} gives exon-level tests for each exon.
\code{"gene"} gives gene-level tests for each gene.
\code{"Simes"} gives genewise p-values derived from the exon-level tests after Simes adjustment for each gene.}
\item{number}{integer, maximum number of rows to output.}
\item{FDR}{numeric, only show exons or genes with false discovery rate less than this cutoff.}
}
\details{
Ranks genes or exons by evidence for differential splicing.
The exon-level tests test for differences between each exon and all the exons for the same gene.
The gene-level tests test for any differences in exon usage between experimental conditions.
The Simes method processes the exon-level p-values to give an overall call of differential splicing for each gene.
It returns the minimum Simes-adjusted p-values for each gene.
The gene-level tests are likely to be powerful for genes in which several exons are differentially splices.
The Simes p-values is likely to be more powerful when only a minority of the exons for a gene are differentially spliced.
The exon-level tests are not recommended for formal error rate control.
}
\value{A data.frame with any annotation columns found in \code{lrt} plus the following columns
\item{NExons}{number of exons if \code{test="Simes"} or \code{"gene"}}
\item{Gene.Exon}{exon annotation if \code{test="exon"}}
\item{logFC}{log-fold change of one exon vs all the exons for the same gene (if \code{test="exon"})}
\item{exon.LR}{LR-statistics for exons (if \code{test="exon"} and the object for \code{diffSpliceDGE} was produced by \code{glmFit})}
\item{exon.F}{F-statistics for exons (if \code{test="exon"} and the object for \code{diffSpliceDGE} was produced by \code{glmQLFit})}
\item{gene.LR}{LR-statistics for genes (if \code{test="gene"} and the object for \code{diffSpliceDGE} was produced by \code{glmFit})}
\item{gene.F}{F-statistics for genes (if \code{test="gene"} and the object for \code{diffSpliceDGE} was produced by \code{glmQLFit})}
\item{P.Value}{p-value}
\item{FDR}{false discovery rate}
}
\author{Yunshun Chen and Gordon Smyth}
\seealso{ \code{\link{diffSpliceDGE}}.}
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