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fixing grl.in with newest version of R, and adding stranded gr.tile #47

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Merged
jrafailov merged 5 commits into from
Mar 3, 2025
Merged

fixing grl.in with newest version of R, and adding stranded gr.tile #47

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4e2ff01
added stranded gr.tile
Oct 22, 2024
11eda91
fixed aggregate call inside grl.in()
ieshghi Mar 3, 2025
0389d70
added stranded gr.tile
Oct 22, 2024
2bbf2ba
fixed aggregate call inside grl.in()
ieshghi Mar 3, 2025
420ee61
Merge branch 'ieshghi' of https://github.com/mskilab-org/gUtils into …
ieshghi Mar 3, 2025
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16 changes: 11 additions & 5 deletions R/gUtils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1408,6 +1408,7 @@ gr.pairflip = function(gr)
#'
#' @param gr \code{GRanges}, \code{seqlengths} or \code{Seqinfo} range to tile. If has \code{GRanges} has overlaps, will reduce first.
#' @param width integer Width of each tile (default = 1e3)
#' @param stranded boolean Whether to reverse order of tiles on negative strand (default = FALSE)
#' @examples
#'
#' ## 10 tiles of width 10
Expand All @@ -1418,7 +1419,7 @@ gr.pairflip = function(gr)
#'
#' @return GRanges with tiled intervals
#' @export
gr.tile = function(gr, width = 1e3)
gr.tile = function(gr, width = 1e3, stranded = FALSE)
{
numw = tile.id = query.id = NULL ## getting past NOTE
if (is(gr, 'data.table')){
Expand All @@ -1441,8 +1442,14 @@ gr.tile = function(gr, width = 1e3)
st = rep(start(gr), ws)
en = rep(end(gr), ws)
strand = rep(as.character(strand(gr)), ws)
dt = data.table(query.id = rep(1:length(gr), ws), tile.id = 1:sum(ws))
dt[, numw := 0:(length(tile.id)-1), by = query.id]
if(stranded){
dt = data.table(query.id = rep(1:length(gr), ws), tile.id = 1:sum(ws),strand=strand)
dt[strand=='+', numw := 0:(length(tile.id)-1), by = query.id]
dt[strand=='-', numw := rev(0:(length(tile.id)-1)), by = query.id]
}else{
dt = data.table(query.id = rep(1:length(gr), ws), tile.id = 1:sum(ws))
dt[, numw := 0:(length(tile.id)-1), by = query.id]
}
start = pmin(st+width*dt$numw, en)
end = pmin(st+width*(dt$numw+1)-1, en)

Expand Down Expand Up @@ -2116,7 +2123,6 @@ grl.in = function(grl, windows, some = FALSE, only = FALSE, logical = TRUE, exac

m$grl.id = gr$grl.ix[m$query.id]
m$grl.iid = gr$grl.iix[m$query.id]

if (some){
tmp = as.data.frame(m[, length(unique(grl.iid)), by = grl.id])
}
Expand All @@ -2126,7 +2132,7 @@ grl.in = function(grl, windows, some = FALSE, only = FALSE, logical = TRUE, exac
split(m$query.id, factor(m$grl.id, 1:length(grl)))))
}
else{
tmp = stats::aggregate(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin-length(setdiff(1:numwin, x)))
tmp = stats::aggregate(x = subject.id ~ grl.id, data = m, FUN = function(x) numwin-length(setdiff(1:numwin, x)))
}

out = rep(FALSE, length(grl))
Expand Down