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## convert_map
## Karl W Broman
# Convert marker map to list for use in interactive plot
#
# Convert a genetic map to format
# for use with interative graphics, such as \code{\link{iplotMap}}.
# (Largely for internal use.)
#
# @param map An object of class \code{"map"}: a list with each
# component being a vector of marker positions
#
# @return Map in special format for using in \code{\link{iplotMap}},
# includes ordered vectors of chromosome IDs, marker positions, and
# marker names, and then the distinct chromosome IDs in order
#
# @keywords interface
#
# @examples
# library(qtl)
# data(hyper)
# map <- pull.map(hyper)
# map_reformatted <- convert_map(map)
convert_map <-
function(map) {
chrnames <- names(map)
# remove the A/X classes
map <- lapply(map, unclass)
chr <- rep(names(map), vapply(map, length, 1))
names(chr) <- NULL
pos <- unlist(map)
names(pos) <- NULL
mnames <- unlist(lapply(map, names))
names(mnames) <- NULL
list(chr=chr, pos=pos, marker=mnames, chrname=chrnames)
}
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