olRanges.RdFunction for identifying consensus peak among two peaks sets sharing a minimum relative overlap.
olRanges(query, subject, output = "gr")Object of class GRanges, which is a vector of genomic locations and associated annotations.
Object of class GRanges.
By default "gr" returns any overlap with OL length information in an object of class GRanges. Also, can returns an object of class data.frame with "df".
## Sample Data Sets
grq <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges = IRanges::IRanges(seq(1, 100, by=10), end = seq(30, 120, by=10)), strand = Rle(strand(c("-", "+", "-")), c(1, 7, 2)))
grs <- shift(grq[c(2,5,6)], 5)
## Run olRanges function
olRanges(query=grq, subject=grs, output="df")
#> space Qindex Sindex Qstart Qend Sstart Send OLstart OLend OLlength OLpercQ
#> 1 chr2 2 1 11 40 16 45 16 40 25 83.33333
#> 2 chr2 3 1 21 50 16 45 21 45 25 83.33333
#> 3 chr2 4 1 31 60 16 45 31 45 15 50.00000
#> 4 chr1 5 2 41 70 46 75 46 70 25 83.33333
#> 5 chr1 5 3 41 70 56 85 56 70 15 50.00000
#> 6 chr1 6 2 51 80 46 75 51 75 25 83.33333
#> 7 chr1 6 3 51 80 56 85 56 80 25 83.33333
#> OLpercS OLtype
#> 1 83.33333 oldown
#> 2 83.33333 olup
#> 3 50.00000 olup
#> 4 83.33333 oldown
#> 5 50.00000 oldown
#> 6 83.33333 olup
#> 7 83.33333 oldown
olRanges(query=grq, subject=grs, output="gr")
#> GRanges object with 7 ranges and 13 metadata columns:
#> seqnames ranges strand | space Qindex Sindex Qstart
#> <Rle> <IRanges> <Rle> | <character> <integer> <integer> <integer>
#> [1] chr2 11-40 + | chr2 2 1 11
#> [2] chr2 21-50 + | chr2 3 1 21
#> [3] chr2 31-60 + | chr2 4 1 31
#> [4] chr1 41-70 + | chr1 5 2 41
#> [5] chr1 41-70 + | chr1 5 3 41
#> [6] chr1 51-80 + | chr1 6 2 51
#> [7] chr1 51-80 + | chr1 6 3 51
#> Qend Sstart Send OLstart OLend OLlength OLpercQ
#> <integer> <integer> <integer> <numeric> <numeric> <numeric> <numeric>
#> [1] 40 16 45 16 40 25 83.3333
#> [2] 50 16 45 21 45 25 83.3333
#> [3] 60 16 45 31 45 15 50.0000
#> [4] 70 46 75 46 70 25 83.3333
#> [5] 70 56 85 56 70 15 50.0000
#> [6] 80 46 75 51 75 25 83.3333
#> [7] 80 56 85 56 80 25 83.3333
#> OLpercS OLtype
#> <numeric> <character>
#> [1] 83.3333 oldown
#> [2] 83.3333 olup
#> [3] 50.0000 olup
#> [4] 83.3333 oldown
#> [5] 50.0000 oldown
#> [6] 83.3333 olup
#> [7] 83.3333 oldown
#> -------
#> seqinfo: 3 sequences from an unspecified genome; no seqlengths