\name{rangeSampleMeans}
\alias{rangeSampleMeans}
\title{Average features in ranges per sample...}
\usage{rangeSampleMeans(query.rd, subject, assay.element)
}
\description{Average features in ranges per sample}
\details{This function takes per-feature genomic data and returns averages for each of a set of genomic ranges.
The most obvious application is determining the copy number of a set of genes. The features
corresponding to each gene are determined with boundingIndices such that all features with the bounds
of a gene (overlaps). The features on either side of the gene unless those positions
exactly match the first or last base covered by the gene.  Therefore, genes falling between two features
will at least cover two features. This is similar to rangeSampleMeans, but it checks the subject
positions for being sorted and not being NA and also treats them as doubles, not ints. Range bounding
performed by the boundingIndices function.}
\value{numeric matrix of features in each range averaged by sample}
\seealso{boundingIndices intervalBound}
\author{Peter M. Haverty}
\arguments{\item{query.rd}{RangedData object representing genomic regions (genes) to be averaged.}
\item{subject}{A GenoSet object or derivative}
\item{assay.element}{character, name of element in assayData to use to extract data}
}
\examples{data(genoset)
my.genes = RangedData( ranges=IRanges(start=c(35e6,128e6),end=c(37e6,129e6),names=c("HER2","CMYC")), space=c("chr17","chr8"), universe="hg19")
rangeSampleMeans( my.genes, baf.ds, "lrr" )}