“`{r}
library(GenomicRanges)
example(GRanges)
mycov <- coverage(longGR, weight=score(longGR))
rle.i <- slice(mycov, lower=1)
gr <- as (rle.i, "GRanges")
gr
```=====EndrmdSourceCode=====
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
##
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
##
## The following object is masked from 'package:stats':
##
## xtabs
##
## The following objects are masked from 'package:base':
##
## Filter, Find, Map, Position, Reduce, anyDuplicated, append,
## as.data.frame, as.vector, cbind, colnames, do.call,
## duplicated, eval, evalq, get, intersect, is.unsorted, lapply,
## mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rep.int, rownames, sapply, setdiff,
## sort, table, tapply, union, unique, unlist, unsplit
##
## Loading required package: S4Vectors
## Loading required package: stats4
## Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
##
## GRangs> seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
##
## GRangs> gr <-
## GRangs+ GRanges(seqnames =
## GRangs+ Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
## GRangs+ ranges = IRanges(
## GRangs+ 1:10, width = 10:1, names = head(letters,10)),
## GRangs+ strand = Rle(
## GRangs+ strand(c("-", "+", "*", "+", "-")),
## GRangs+ c(1, 2, 2, 3, 2)),
## GRangs+ score = 1:10,
## GRangs+ GC = seq(1, 0, length=10),
## GRangs+ seqinfo=seqinfo)
##
## GRangs> gr
## GRanges object with 10 ranges and 2 metadata columns:
## seqnames ranges strand | score GC
## <Rle> <IRanges> <Rle> | <integer> <numeric>
## a chr1 [ 1, 10] - | 1 1
## b chr2 [ 2, 10] + | 2 0.888888888888889
## c chr2 [ 3, 10] + | 3 0.777777777777778
## d chr2 [ 4, 10] * | 4 0.666666666666667
## e chr1 [ 5, 10] * | 5 0.555555555555556
## f chr1 [ 6, 10] + | 6 0.444444444444444
## g chr3 [ 7, 10] + | 7 0.333333333333333
## h chr3 [ 8, 10] + | 8 0.222222222222222
## i chr3 [ 9, 10] - | 9 0.111111111111111
## j chr3 [10, 10] - | 10 0
## -------
## seqinfo: 3 sequences from mock1 genome
##
## GRangs> ## Summarizing elements
## GRangs> table(seqnames(gr))
##
## chr1 chr2 chr3
## 3 3 4
##
## GRangs> sum(width(gr))
## [1] 55
##
## GRangs> summary(mcols(gr)[,"score"])
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.00 3.25 5.50 5.50 7.75 10.00
##
## GRangs> ## Renaming the underlying sequences
## GRangs> seqlevels(gr)
## [1] "chr1" "chr2" "chr3"
##
## GRangs> seqlevels(gr) <- sub("chr", "Chrom", seqlevels(gr))
##
## GRangs> gr
## GRanges object with 10 ranges and 2 metadata columns:
## seqnames ranges strand | score GC
## <Rle> <IRanges> <Rle> | <integer> <numeric>
## a Chrom1 [ 1, 10] - | 1 1
## b Chrom2 [ 2, 10] + | 2 0.888888888888889
## c Chrom2 [ 3, 10] + | 3 0.777777777777778
## d Chrom2 [ 4, 10] * | 4 0.666666666666667
## e Chrom1 [ 5, 10] * | 5 0.555555555555556
## f Chrom1 [ 6, 10] + | 6 0.444444444444444
## g Chrom3 [ 7, 10] + | 7 0.333333333333333
## h Chrom3 [ 8, 10] + | 8 0.222222222222222
## i Chrom3 [ 9, 10] - | 9 0.111111111111111
## j Chrom3 [10, 10] - | 10 0
## -------
## seqinfo: 3 sequences from mock1 genome
##
## GRangs> seqlevels(gr) <- sub("Chrom", "chr", seqlevels(gr)) # revert
##
## GRangs> ## Combining objects
## GRangs> gr2 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 3, 4)),
## GRangs+ IRanges(1:10, width=5), strand='-',
## GRangs+ score=101:110, GC = runif(10),
## GRangs+ seqinfo=seqinfo)
##
## GRangs> gr3 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 4, 3)),
## GRangs+ IRanges(101:110, width=10), strand='-',
## GRangs+ score=21:30,
## GRangs+ seqinfo=seqinfo)
##
## GRangs> some.gr <- c(gr, gr2)
##
## GRangs> ## all.gr <- c(gr, gr2, gr3) ## (This would fail)
## GRangs> all.gr <- c(gr, gr2, gr3, ignore.mcols=TRUE)
##
## GRangs> ## Subsetting a named list-like object *by* a GRanges subscript
## GRangs> x <- RleList(chr1=101:120, chr2=2:-8, chr3=31:40)
##
## GRangs> x[gr]
## RleList of length 10
## $chr1
## integer-Rle of length 10 with 10 runs
## Lengths: 1 1 1 1 1 1 1 1 1 1
## Values : 101 102 103 104 105 106 107 108 109 110
##
## $chr2
## integer-Rle of length 9 with 9 runs
## Lengths: 1 1 1 1 1 1 1 1 1
## Values : 1 0 -1 -2 -3 -4 -5 -6 -7
##
## $chr2
## integer-Rle of length 8 with 8 runs
## Lengths: 1 1 1 1 1 1 1 1
## Values : 0 -1 -2 -3 -4 -5 -6 -7
##
## $chr2
## integer-Rle of length 7 with 7 runs
## Lengths: 1 1 1 1 1 1 1
## Values : -1 -2 -3 -4 -5 -6 -7
##
## $chr1
## integer-Rle of length 6 with 6 runs
## Lengths: 1 1 1 1 1 1
## Values : 105 106 107 108 109 110
##
## ...
## <5 more elements>
##
## GRangs> ## The number of lines displayed in the 'show' method
## GRangs> ## are controlled with two global options.
## GRangs> longGR <- c(gr[,"score"], gr2[,"score"], gr3)
##
## GRangs> longGR
## GRanges object with 30 ranges and 1 metadata column:
## seqnames ranges strand | score
## <Rle> <IRanges> <Rle> | <integer>
## a chr1 [1, 10] - | 1
## b chr2 [2, 10] + | 2
## c chr2 [3, 10] + | 3
## d chr2 [4, 10] * | 4
## e chr1 [5, 10] * | 5
## ... ... ... ... ... ...
## chr2 [106, 115] - | 26
## chr2 [107, 116] - | 27
## chr3 [108, 117] - | 28
## chr3 [109, 118] - | 29
## chr3 [110, 119] - | 30
## -------
## seqinfo: 3 sequences from mock1 genome
##
## GRangs> options("showHeadLines"=7)
##
## GRangs> options("showTailLines"=2)
##
## GRangs> longGR
## GRanges object with 30 ranges and 1 metadata column:
## seqnames ranges strand | score
## <Rle> <IRanges> <Rle> | <integer>
## a chr1 [1, 10] - | 1
## b chr2 [2, 10] + | 2
## c chr2 [3, 10] + | 3
## d chr2 [4, 10] * | 4
## e chr1 [5, 10] * | 5
## f chr1 [6, 10] + | 6
## g chr3 [7, 10] + | 7
## ... ... ... ... ... ...
## chr3 [109, 118] - | 29
## chr3 [110, 119] - | 30
## -------
## seqinfo: 3 sequences from mock1 genome
##
## GRangs> ## Revert to default values
## GRangs> options("showHeadLines"=NULL)
##
## GRangs> options("showTailLines"=NULL)
mycov <- coverage(longGR, weight=score(longGR))
rle.i <- slice(mycov, lower=1)
gr <- as (rle.i, "GRanges")
gr
## GRanges object with 39 ranges and 2 metadata columns:
## seqnames ranges strand | score view
## <Rle> <IRanges> <Rle> | <integer> <integer>
## [1] chr1 [1, 1] * | 102 1
## [2] chr1 [2, 2] * | 204 1
## [3] chr1 [3, 4] * | 307 1
## [4] chr1 [5, 5] * | 312 1
## [5] chr1 [6, 6] * | 217 1
## ... ... ... ... ... ... ...
## [35] chr3 [108, 108] * | 28 2
## [36] chr3 [109, 109] * | 57 2
## [37] chr3 [110, 117] * | 87 2
## [38] chr3 [118, 118] * | 59 2
## [39] chr3 [119, 119] * | 30 2
## -------
## seqinfo: 3 sequences from an unspecified genome; no seqlengths
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