Ranges represent: - Data, e.g., aligned reads, ChIP peaks, SNPs, CpG islands, … - Annotations, e.g., gene models, regulatory elements, methylated regions - Ranges are defined by chromosome, start, end, and strand - Often, metadata is associated with each range, e.g., quality of alignment, strength of ChIP peak
Many common biological questions are range-based - What reads overlap genes? - What genes are ChIP peaks nearest? - …
Range operations
Ranges - IRanges - start() / end() / width() - List-like – length(), subset, etc. - ‘metadata’, mcols() - GRanges - ‘seqnames’ (chromosome), ‘strand’ - Seqinfo, including seqlevels and seqlengths
Intra-range methods - Independent of other ranges in the same object - GRanges variants strand-aware - shift(), narrow(), flank(), promoters(), resize(), restrict(), trim() - See ?"intra-range-methods"
Inter-range methods - Depends on other ranges in the same object - range(), reduce(), gaps(), disjoin() - coverage() (!) - see ?"inter-range-methods"
Between-range methods - Functions of two (or more) range objects - findOverlaps(), countOverlaps(), …, %over%, %within%, %outside%; union(), intersect(), setdiff(), punion(), pintersect(), psetdiff()
Example
require(GenomicRanges)
gr <- GRanges("A", IRanges(c(10, 20, 22), width=5), "+")
shift(gr, 1) # 1-based coordinates!
## GRanges object with 3 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] A [11, 15] +
## [2] A [21, 25] +
## [3] A [23, 27] +
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengths
range(gr) # intra-range
## GRanges object with 1 range and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] A [10, 26] +
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengths
reduce(gr) # inter-range
## GRanges object with 2 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] A [10, 14] +
## [2] A [20, 26] +
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengths
coverage(gr)
## RleList of length 1
## $A
## integer-Rle of length 26 with 6 runs
## Lengths: 9 5 5 2 3 2
## Values : 0 1 0 1 2 1
setdiff(range(gr), gr) # 'introns'
## GRanges object with 1 range and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] A [15, 19] +
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengths
IRangesList, GRangesList - List: all elements of the same type - Many *List-aware methods, but a common ‘trick’: apply a vectorized function to the unlisted representaion, then re-list
grl <- GRangesList(...)
orig_gr <- unlist(grl)
transformed_gr <- FUN(orig)
transformed_grl <- relist(, grl)
Reference
- Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi:10.1371/journal.pcbi.1003118
