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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/correlateGenes.R
\name{correlateGenes}
\alias{correlateGenes}
\title{Per-gene correlation statistics}
\usage{
correlateGenes(stats)
}
\arguments{
\item{stats}{A \linkS4class{DataFrame} of pairwise correlation statistics, returned by \code{\link{correlatePairs}}.}
}
\value{
A \linkS4class{DataFrame} with one row per unique gene in \code{stats} and containing the fields:
\describe{
\item{\code{gene}:}{A field of the same type as \code{stats$gene1} specifying the gene identity.}
\item{\code{rho}:}{Numeric, the correlation with the largest magnitude across all gene pairs involving the corresponding gene.}
\item{\code{p.value}:}{Numeric, the Simes p-value for this gene.}
\item{\code{FDR}:}{Numeric, the adjusted \code{p.value} across all rows.}
\item{\code{limited}:}{Logical, indicates whether the combined p-value is at its lower bound.}
}
}
\description{
Compute per-gene correlation statistics by combining results from gene pair correlations.
}
\details{
For each gene, all of its pairs are identified and the corresponding p-values are combined using Simes' method.
This tests whether the gene is involved in significant correlations to \emph{any} other gene.
Per-gene statistics are useful for identifying correlated genes without regard to what they are correlated with (e.g., during feature selection).
}
\examples{
library(scuttle)
sce <- mockSCE()
sce <- logNormCounts(sce)
pairs <- correlatePairs(sce, iters=1e5, subset.row=1:100)
g.out <- correlateGenes(pairs)
head(g.out)
}
\references{
Simes RJ (1986).
An improved Bonferroni procedure for multiple tests of significance.
\emph{Biometrika} 73:751-754.
}
\seealso{
\code{\link{correlatePairs}}, to compute \code{stats}.
}
\author{
Aaron Lun
}
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