# insert_pseudomarkers
#' Insert pseudomarkers into a marker map
#'
#' Insert pseudomarkers into a map of genetic markers, for a single chromosome.
#'
#' @md
#'
#' @param map A list of numeric vectors; each vector gives marker
#' positions for a single chromosome.
#' @param step Distance between pseudomarkers and markers; if
#' `step=0` no pseudomarkers are inserted.
#' @param off_end Distance beyond terminal markers in which to insert
#' pseudomarkers.
#' @param stepwidth Indicates whether to use a fixed grid
#' (`stepwidth="fixed"`) or to use the maximal distance between
#' pseudomarkers to ensure that no two adjacent markers/pseudomarkers
#' are more than `step` apart.
#' @param pseudomarker_map A map of pseudomarker locations; if provided the
#' `step`, `off_end`, and `stepwidth` arguments are
#' ignored.
#' @param tol Tolerance for determining whether a pseudomarker would duplicate a marker position.
#' @param cores Number of CPU cores to use, for parallel calculations.
#' (If `0`, use [parallel::detectCores()].)
#' Alternatively, this can be links to a set of cluster sockets, as
#' produced by [parallel::makeCluster()].
#'
#' @return A list like the input `map` with pseudomarkers
#' inserted. Will also have an attribute `"is_x_chr"`, taken
#' from the input `map`.
#'
#' @details If `stepwidth="fixed"`, a grid of pseudomarkers is
#' added to the marker map.
#'
#' If `stepwidth="max"`, a minimal set of pseudomarkers are
#' added, so that the maximum distance between adjacent markers or
#' pseudomarkers is at least `step`. If two adjacent markers are
#' separated by less than `step`, no pseudomarkers will be added
#' to the interval. If they are more then `step` apart, a set of
#' equally-spaced pseudomarkers will be added.
#'
#' If `pseudomarker_map` is provided, then the `step`,
#' `off_end`, and `stepwidth` arguments are ignored, and the
#' input `pseudomarker_map` is taken to be the set of
#' pseudomarker positions.
#'
#' @export
#' @keywords utilities
#' @seealso [calc_genoprob()], [calc_grid()]
#'
#' @examples
#' iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
#' gmap_w_pmar <- insert_pseudomarkers(iron$gmap, step=1)
insert_pseudomarkers <-
function(map, step=0, off_end=0, stepwidth=c("fixed", "max"),
pseudomarker_map=NULL, tol=0.01, cores=1)
{
if(is.null(map))
stop("Input map is NULL")
# is input not a map but a cross2 object?
cl <- class(map)
if(length(cl)==1 && cl=="cross2") {
map <- map$gmap
if(is.null(map))
stop("Input is a cross2 object, but no genetic map found.")
}
# check inputs
stepwidth <- match.arg(stepwidth)
if(is.null(pseudomarker_map)) {
pseudomarker_map <- vector("list", length(map))
}
else {
if(!is.list(pseudomarker_map))
stop("pseudomarker_map should be a list")
if(length(pseudomarker_map) != length(map))
stop("length(pseudomarker_map) != length(map)")
}
chr <- names(map)
# set up cluster
cores <- setup_cluster(cores)
# do the work, possible with multiple CPU
newmap <- cluster_lapply(cores, seq(along=map), function(i)
insert_pseudomarkers_onechr(map[[i]], step=step, off_end=off_end, stepwidth=stepwidth,
pseudomarker_map[[i]], tol=tol, paste0("c", chr[i], ".loc")))
names(newmap) <- chr
attr(newmap, "is_x_chr") <- attr(map, "is_x_chr")
newmap
}
insert_pseudomarkers_onechr <-
function(map, step=0, off_end=0, stepwidth=c("fixed", "max"),
pseudomarker_map=NULL, tol=0.01, pmar_stem="loc")
{
if(any(is.na(map))) stop("map values can't be missing")
if(tol < 0) stop("tol should be >= 0")
if(is.null(pseudomarker_map)) {
stepwidth <- match.arg(stepwidth)
if(step < 0) stop("step should be >= 0")
if(step > 0 && tol >= step) stop("tol should be << step")
if(off_end < 0) stop("off_end should be >= 0")
}
else {
if(any(is.na(pseudomarker_map)))
stop("pseudomarker_map values can't be missing")
stepwidth <- "custom"
}
switch(stepwidth,
fixed=insert_pseudomarkers_grid(map, step, off_end, tol, pmar_stem),
max=insert_pseudomarkers_minimal(map, step, off_end, tol, pmar_stem),
custom=combine_markers_with_pseudomarkers(map, pseudomarker_map, tol, pmar_stem))
}
# pseudomarker map as grid, ignoring markers
#
# map = vector of marker positions; names = marker names
# step = distance between pseudomarkers
# off_end = amount to go beyond the terminal markers
# tol = tolerance for determining whether a marker hits a pseudomarker
# pmar_stem = leading part of name of pseudomarkers
insert_pseudomarkers_grid <-
function(map, step, off_end=0, tol=0.01, pmar_stem="loc")
{
if(step==0) return(map)
# locations of pseudomarkers
pmar <- seq(min(map)-off_end, max(map)+off_end, by=step)
combine_markers_with_pseudomarkers(map, pmar, tol, pmar_stem, step)
}
# combine the markers in "map" with the pseudomarker positions in
# "pmar". treat the positions in "pmar" as a grid, and return a
# logical vector of which values in output are on the grid.
combine_markers_with_pseudomarkers <-
function(map, pmar_map, tol=0.01, pmar_stem="loc", step=0.1)
{
# for each pseudomarker, distance to nearest marker
d <- abs(outer(map, pmar_map, "-"))
mind <- apply(d, 2, min)
# omit pseudomarkers that hit a marker
to_omit <- (mind < tol)
pmar_map <- pmar_map[!to_omit]
if(length(pmar_map) == 0) return(map)
if(is.null(names(pmar_map)))
names(pmar_map) <- create_pseudomarker_names(pmar_map, step, pmar_stem)
# add pseudomarkers to markers and sort
sort(c(map, pmar_map))
}
# create names for pseudomarkers
create_pseudomarker_names <-
function(pmar_map, step, pmar_stem="loc")
{
digits <- ceiling(-log10(step))
digits <- ifelse(digits < 0, 0, digits)
pmar_nam <- paste0(pmar_stem, round(pmar_map, digits))
while(any_duplicates(pmar_nam)) {
digits <- digits + 1
pmar_nam <- paste0(pmar_stem, round(pmar_map, digits))
}
pmar_nam
}
any_duplicates <-
function(x)
length(unique(x)) < length(x)
# pseudomarker map, minimal number of pseudomarkers to add
#
# map = vector of marker positions; names = marker names
# step = min distance between markers or pseudomarkers
# off_end = amount to go beyond the terminal markers
# tol = tolerance for determining whether a marker hits a pseudomarker
# pmar_stem = leading part of name of pseudomarkers
insert_pseudomarkers_minimal <-
function(map, step, off_end=0, tol=0.01, pmar_stem="loc")
{
if(step==0) return(map)
# distance between markers
d <- diff(map)
if(any(d < 0))
stop("marker positions should be sorted")
pmar_map <- c(seq(min(map), min(map)-off_end, by=-step)[-1],
seq(max(map), max(map)+off_end, by=step)[-1])
if(length(map) == 1) { # just one marker
map <- c(map, pmar_map)
o <- order(map)
map <- map[o]
return(map)
}
# intervals needing pseudomarkers (d = distances between adjacent markers
int2fill <- which(d > step)
pmar_map <- c(pmar_map, unlist(lapply(int2fill, function(a) {
n <- ceiling((map[a+1]-map[a])/step)+1
seq(map[a], map[a+1], length.out=n)[-c(1, n)] })))
if(length(pmar_map) == 0) {
return(map)
}
names(pmar_map) <- create_pseudomarker_names(pmar_map, step, pmar_stem)
# add pseudomarkers to markers and sort
sort(c(map, pmar_map))
}
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