Genomic Ranges

Hervé Pagès, Martin Morgan
February 4, 2015

A quick introduction to GRanges and GRangesList objects

See slides.

Recall: Genomic Ranges

• GRanges

  

• GRangesList

  

CompressedList

• GRangesList inherits from CompressedList

  library(GenomicRanges)
  showClass("GRangesList")
  

  ## Class "GRangesList" [package "GenomicRanges"]
  ## 
  ## Slots:
  ##                                                             
  ## Name:         unlistData   elementMetadata      partitioning
  ## Class:           GRanges         DataFrame PartitioningByEnd
  ##                                           
  ## Name:        elementType          metadata
  ## Class:         character              list
  ## 
  ## Extends: 
  ## Class "CompressedList", directly
  ## Class "GenomicRangesList", directly
  ## Class "GenomicRangesORGRangesList", directly
  ## Class "List", by class "CompressedList", distance 2
  ## Class "Vector", by class "CompressedList", distance 3
  ## Class "Annotated", by class "CompressedList", distance 4
  

• Consequences: unlist() and relist() are very cheap. The unlist() / relist() pattern can be used in many situations where looping over the GRangesList would be inefficient.

• Example:

  library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
  

  ## Loading required package: GenomicFeatures
  ## Loading required package: AnnotationDbi
  ## Loading required package: Biobase
  ## Welcome to Bioconductor
  ## 
  ##     Vignettes contain introductory material; view with
  ##     'browseVignettes()'. To cite Bioconductor, see
  ##     'citation("Biobase")', and for packages 'citation("pkgname")'.
  ## 
  ## 
  ## Attaching package: 'AnnotationDbi'
  ## 
  ## The following object is masked from 'package:GenomeInfoDb':
  ## 
  ##     species
  

  txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
  tx_by_gn <- transcriptsBy(txdb, by="gene")
  unlisted <- unlist(tx_by_gn)
  TSS <- ifelse(strand(unlisted) == "+", start(unlisted), end(unlisted))
  TSS <- GRanges(seqnames(unlisted), IRanges(TSS, width=1), strand(unlisted))
  TSS_by_gn <- relist(TSS, tx_by_gn)
  mcols(TSS) <- mcols(unlisted)
  TSS_by_gn <- relist(TSS, tx_by_gn) 
  

Exercises

See HOWTOs vignette in the GenomicRanges package

• e.g., Exercise 2.12 (using RNAseqData.HNRNPC.bam.chr14), 2.13, 2.16