##'@title Get adjacent markers within a distance around the given marker
##'@description Returns markers adjacent to a given marker (within a preset distance).
##'@author Marcin Kierczak <\email{Marcin.Kierczak@@imbim.uu.se}>
##'@param data a gwaa.data class object as used by the \code{\link[GenABEL]{gwaa.data-class}},
##'@param marker a name of the central marker,
##'@param size.bp window size in basepairs,
##'@return a matrix of marker adjacency
##'@keywords adjacent markers
##'@examples
##'\dontrun{
##' adj.markers <- get.adjacent.markers(data, 'BICF2P647127')
##' }
##'@export
get.adjacent.markers <- function(data, marker, size.bp=1e3) {
chr <- data@gtdata@chromosome[marker]
chr.data <- data[,which(data@gtdata@chromosome == chr)]
coord <- chr.data@gtdata@map[marker]
start <- pmax(min(chr.data@gtdata@map), coord - size.bp)
end <- pmin(coord + size.bp, max(chr.data@gtdata@map))
tmp <- chr.data[,which(chr.data@gtdata@map >= start & chr.data@gtdata@map <= end)]
return(as.double(tmp@gtdata))
}
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