class: center, middle, inverse, title-slide # Genomic ranges ### Mikhail Dozmorov ### Virginia Commonwealth University ### 02-24-2021 --- class: center, middle # Data representation in R / Bioconductor --- ## Ranges overview .center[ <img src="img/RangeOperations.png" height = 550> ] --- ## Ranges in Bioconductor - IRanges - `start()` / `end()` / `width()` - List-like -- `length()`, subset, etc. - 'metadata', `mcols()` - GRanges - 'seqnames' (chromosome), 'strand' - `Seqinfo`, including `seqlevels` and `seqlengths` --- ## Range methods - Intra-range methods: See `?"intra-range-methods"` - Independent of other ranges in the same object - `shift()`, `narrow()`, `flank()`, `promoters()`, `resize()`, `trim()` - Inter-range methods: See `?"inter-range-methods"` - Depends on other ranges in the same object - `range()`, `reduce()`, `gaps()`, `disjoin()`, `coverage()` - Between-range methods - Functions of two (or more) range objects - `findOverlaps()`, `countOverlaps()`, `summarizeOverlaps()`, ..., `%over%`, `%within%`, `%outside%`, `union()`, `intersect()`, `setdiff()`, `punion()`, `pintersect()`, `psetdiff()` --- ## IRanges - The `IRanges` package defines an important class for specifying integer ranges - There are many interesting operations to be performed on ranges, e.g, `flank()` identifies adjacent ranges - `IRanges` extends the `Ranges` class --- ## Genomic Ranges The `GenomicRanges` package extends the notion of ranges to include features relevant to application of ranges in sequence analysis, particularly the ability to associate a range with a sequence name (e.g., chromosome) and a strand. .center[ <img src="img/GRanges.png" height = 380> ] --- ## GenomicRanges - Data (e.g., aligned reads, called peaks, copy number) - Annotations (e.g., genes, exons, transcripts) - Close relation to BED files (see `rtracklayer::import.bed()` and `HelloRanges`) - Also vector interface – `length()`, `[`, etc. --- ## Lists of Genomic Ranges - List definition - all elements of the same type - E.g., lists of exons-within-transcripts, alignments-within-reads - Many *List-aware methods, but a common ‘trick’: apply a vectorized function to the unlisted representaion, then re-list .small[ Lawrence M, Huber W, Pag&egrave;s H, Aboyoun P, Carlson M, et al. (2013) [Software for Computing and Annotating Genomic Ranges](https://doi.org/10.1371/journal.pcbi.1003118). PLoS Comput Biol ] --- ## Lists of Genomic Ranges .center[ <img src="img/GRangesList.png" height = 550> ]