collapseAt.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/collapseAt.R
\name{collapseAt}
\alias{collapseAt}
\title{Collapse a SummarizedExperiment-like object over a GRanges, sensibly.
Handy for things like chromophobe model testing, GenometriCorr, etc.}
\usage{
collapseAt(x, y, how = c("median", "mean", "sum"), BPPARAM = SerialParam())
}
\arguments{
\item{x}{something descended from SummarizedExperiment, with assays()}

\item{y}{something descended from a GRanges, with a granges() method}

\item{how}{how to summarize the assay values (default: median)}

\item{BPPARAM}{BPPARAM object to run in parallel (default: SerialParam())}
}
\value{
an object with same colData but with new rowData and assays
}
\description{
Collapse a SummarizedExperiment-like object over a GRanges, sensibly.
Handy for things like chromophobe model testing, GenometriCorr, etc.
}
\details{
TODO: let the user provide their own summarizer function
}
\examples{

set.seed(123)
rr <- as(c("chr8:11657801-11665899","chr8:11665900-11700200"), "GRanges")
cd <- DataFrame(sample=letters[1:4], treatment=c(0,1,0,1))
rownames(cd) <- cd$sample
beta <- matrix(runif(8), nrow=length(rr), ncol=nrow(cd), 
               dimnames=list(as.character(rr), rownames(cd)))
tpm <- matrix(exp(rnorm(8)), nrow=length(rr), ncol=nrow(cd), 
              dimnames=list(as.character(rr), rownames(cd)))
se <- SummarizedExperiment(list(beta=beta,tpm=tpm), rowRanges=rr, colData=cd)
gr <- as("chr8:11665843-11665969", "GRanges")
collapseAt(se, gr)

}