Genomics Ranges

Some specific data structures are been developped by Bioconductor team:

ExpressionSet/methylSet: Matrix-like dataset plus experiment/sample/feature metadata.. SummarizedExperiment: Analogous to ExpressionSet, but features defined in genomic coordinates. GRanges :Genomic coordinates and associated qualitative and quantitative information, e. g., gene symbol, coverage, p-value.

S3 and S4 structures: particular structures in R to manage a complex data structure.

Lawrence M, Huber W, PagEs H, Aboyoun P, Carlson M, Gentleman R, Morgan M and Carey V (2013).
“Software for Computing and Annotating Genomic Ranges.”
PLoS Computational Biology, 9.

Available here

• manipulate efficently genomic annotations and alignments in high-throughput data
  
• store informations such as genomic intervals, score …

• Iranges, describes one interval
  
• Granges, describes one transcript (for exemple)
  
• GrangesList, describes all transcripts of a given gene (for exemple)
  

seqnames: define the chromosome
ranges: define the boundaries of the element ( gene, exons, TFBS…). start/end
strand : +/-/*

Note1: the start is always the left position and the end the right, even when the range is on the minus strand.
Note2: seqnames/interval/strand are used for Granges objects comparison.

Extra column of informations. accessor mcols()

GRanges objects are considered vector-like objects

• length()
• names()
• subsetting
• c()
• comparison : ==, !=, match(), %in%, duplicated(), unique() …

storing a list of compatible GRanges objects.

Compatible : relative to the same genome same metadata columns

GRanges objects are considered list-like objects

Some functions work very well with this kind of list: elementLengths(GRangeList obj) shift() reduce() …

here