microhomology.RdComputes microhomology at 5bp, 10bp, 50bp, and 100bp windows around ALT junctions of input gGraph (or Junction object) gg and adds these as an edge annotation to the appropriate edges.
microhomology(
gg,
hg,
prefix_only = FALSE,
pad = c(5, 10, 50, 100),
ignore_missing = FALSE
)gGraph or Junctions
DNAStringSet or path to reference fasta
(logical) default FALSE. if TRUE, considers only the longest common prefix. if FALSE, considers the longest local alignment.
(numeric) default NA (use the default window lengths of 5, 10, 50, and 100). otherwise, an integer specifying window length.
(logical) ignore junctions where at least one breakend is not found on the reference, and return -1 for microhomology. default FALSE, which will cause an error.
gGraph with $pyrgo marking on nodes and edges labeling unique "events"
The default behavior is to compute the maximum microhomology using local alignment across the entire window. However, the longest common prefix within each window can be specified by setting the argument prefix_only to TRUE.
Care should be taken that the sequence names of junctions are consistent with those provided in the reference. There will be an error if the sequence names of the junction are not a subset of those of the reference, if ignore_missing is FALSE (default). If ignore_missing is TRUE, then those junctions with missing seqnames will be assigned score -1.
Requires Biostrings.