annotateInteractions: Annotate interactions
In LTLA/fugi: Further Utilities for Genomic Interactions

Description Usage Arguments Details Value Examples

This function will annotate the interactions in a GenomicInteractions object with node class information.

annotateInteractions(GIObject, annotations)

## S4 method for signature 'GenomicInteractions,list'
annotateInteractions(GIObject,
  annotations)

`GIObject`	A GenomicInteractions object to be annotated.
`annotations`	A list containing GRanges (or GRangesList) objects to be used to annotate `GIObject`.

For each interaction, this function identifies the entries of annotations that overlap an anchor region. For each entry in annotations, a metadata column is added to the GenomicInteractions object, containing a list that specifies the elements inside the entry that overlap each interaction. The metadata column is named as NAME.id where NAME is the name of the entry. Anonymous lists will be given names FEATURE#.id where # is the position in the list.

For each anchor, a node.class metadata column will also be added, containing the name of the list element which was first annotated to each range. Ranges with no overlaps will be classified as "distal". The identifiers for each individual feature/annotation are taken from either the name of the list item in the case of a GRangesList or from either the names of a the provided GRanges or an id column in its associated metadata.

NULL is invisibly returned, while the value passed as GIObject is modified in the global namespace.

data(hic_example_data)
hic_example_data <- updateObject(hic_example_data)
mcols(regions(hic_example_data, type=1))

data(mm9_refseq_promoters)
mm9_refseq_grl <- split(mm9_refseq_promoters, mm9_refseq_promoters$id)
annotateInteractions(hic_example_data, list(promoter=mm9_refseq_grl))
mcols(regions(hic_example_data, type=1))