\name{getGRanges}
\alias{getGRanges}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
acquire a GRanges instance with eQTL scores for all SNP for a given gene
}
\description{
acquire a GRanges instance with eQTL scores for all SNP for a given gene
}
\usage{
getGRanges(mgr, ffind, geneind, seqnames, namedlocs)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{mgr}{
instance of \code{\link{eqtlTestsManager-class}}
}
  \item{ffind}{
index into the list of \code{ff} files that are being managed, typically
a sequential index into the list of chromosomes analyzed
}
  \item{geneind}{
identifier or index of gene of interest
}
  \item{seqnames}{
chromosome name
}
  \item{namedlocs}{
a named vector of integer locations, as generated by \code{getNamedLocs} for example
}
}
%\details{
%%%  ~~ If necessary, more details than the description above ~~
%}
%\value{
%%%  ~Describe the value returned
%%%  If it is a LIST, use
%%%  \item{comp1 }{Description of 'comp1'}
%%%  \item{comp2 }{Description of 'comp2'}
%%% ...
%}
%\references{
%%% ~put references to the literature/web site here ~
%}
%\author{
%%%  ~~who you are~~
%}
%\note{
%%%  ~~further notes~~
%}

%% ~Make other sections like Warning with \section{Warning }{....} ~

%\seealso{
%%% ~~objects to See Also as \code{\link{help}}, ~~~
%}
\examples{
if (require("SNPlocs.Hsapiens.dbSNP.20100427")) {
 if (!exists("hmceuB36.2021")) data(hmceuB36.2021)
 library(illuminaHumanv1.db)
 cptag = get("CPNE1", revmap(illuminaHumanv1SYMBOL))
 indc = which(featureNames(hmceuB36.2021) == cptag[1])
 hm = hmceuB36.2021[c(indc,1:19),]  # reduce problem
 td = tempdir()
 curd = getwd()
 setwd(td)
 time.lapply = unix.time(e1 <- eqtlTests( hm, ~male, targdir="ggr" ))
 ggg = getGRanges(e1, 1, cptag, "ch20", 
   getNamedLocs(slpack="SNPlocs.Hsapiens.dbSNP.20100427", chr="ch20"))
 ggg
# now combine with cis ranges for a set of genes
 example(cisRanges)
 cc = cisRanges(m1[1:10], "chr20", "illuminaHumanv1.db")
 seqnames(cc) = "ch20"
 FF = findOverlaps(ggg, cc) 
 GG = split(FF@matchMatrix[,1], FF@matchMatrix[,2]) 
 names(GG) = m1[1:10]
 sapply(GG,length)
 myl = lapply(GG, function(x) ggg[x, ])
 names(myl)
 sapply(myl, function(x) max(elementMetadata(x)$score))

 }
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ models }