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Create similarity matrix from shared exons

create_similarity_from_exons.Rd

Helper function to create an isoform similarity matrix based on shared exons. Uses Jaccard similarity: |A ∩ B| / |A ∪ B|

Usage

create_similarity_from_exons(
  exon_list,
  method = c("jaccard", "overlap", "count")
)

Arguments

exon_list

named list where each element is a character vector of exon IDs for that isoform. Names should match isoform/transcript IDs.

method

character, similarity method: "jaccard" (default), "overlap", or "count"

Value

symmetric similarity matrix

Details

Methods:

  • "jaccard": Jaccard index = |shared| / |union|

  • "overlap": Overlap coefficient = |shared| / min(|A|, |B|)

  • "count": Raw count of shared exons