|
|
@@ -148,30 +148,30 @@
|
|
|
{
|
|
|
stopifnot(is(bins, "GRanges"))
|
|
|
stopifnot(is(numvar, "RleList"))
|
|
|
- stopifnot(identical(seqlevels(bins), names(numvar)))
|
|
|
- bins_per_chrom <- split(ranges(bins), GenomicRanges::seqnames(bins))
|
|
|
+ stopifnot(identical(GenomeInfoDb::seqlevels(bins), names(numvar)))
|
|
|
+ bins_per_chrom <- split(GenomicRanges::ranges(bins), GenomicRanges::seqnames(bins))
|
|
|
sums_list <- lapply(names(numvar),
|
|
|
function(seqname) {
|
|
|
- views <- Views(numvar[[seqname]],
|
|
|
+ views <- IRanges::Views(numvar[[seqname]],
|
|
|
bins_per_chrom[[seqname]])
|
|
|
- viewMeans(views)
|
|
|
+ IRanges::viewMeans(views)
|
|
|
})
|
|
|
new_mcol <- unsplit(sums_list, as.factor(GenomicRanges::seqnames(bins)))
|
|
|
- mcols(bins)[[mcolname]] <- new_mcol
|
|
|
- bins
|
|
|
+ GenomicRanges::mcols(bins)[[mcolname]] <- new_mcol
|
|
|
+ return(bins)
|
|
|
}
|
|
|
|
|
|
|
|
|
GR = GenomicRanges::makeGRangesFromDataFrame(feature_track_chr, keep.extra.columns=TRUE)
|
|
|
GR_chrs = split(GR, GenomicRanges::seqnames(GR))
|
|
|
- seq_lens = sapply(GR_chrs, function(v) max(end(v)))
|
|
|
+ seq_lens = sapply(GR_chrs, function(v) max(GenomicRanges::end(v)))
|
|
|
|
|
|
GR_RleList = GenomicRanges::coverage(GR, weight="score")
|
|
|
seq_info = GenomicRanges::seqinfo(GR_RleList)
|
|
|
GenomeInfoDb::seqlengths(seq_info) = seq_lens
|
|
|
|
|
|
bins = GenomicRanges::tileGenome(seq_info, tilewidth=bin_size, cut.last.tile.in.chrom=TRUE)
|
|
|
- bins = bins[width(bins)==bin_size]
|
|
|
+ bins = bins[GenomicRanges::width(bins)==bin_size]
|
|
|
bin_val_tmp = binnedMean(bins, GR_RleList, "bin_val")
|
|
|
bin_val_tmp = data.table::as.data.table(bin_val_tmp)
|
|
|
bin_val = data.table::data.table(chr=bin_val_tmp$seqnames, bin_index=bin_val_tmp$end / bin_size, continous_rank=log2(1 + bin_val_tmp$bin_val - min(bin_val_tmp$bin_val)))
|
lucananni93