Get sequence matches as a data.frame — .get_match

This function will perform the siRNA sequence match to the transcript library and return it as a data.frame of ranges. This function uses vmatchPattern to perform the matching. The data.frame will have the columns: "names", "start", "end", "width", "seed". If the optional sirna.name argument is provided then an additional column will be added.

Usage

.get_match_df(
  target.seq,
  seqs,
  seed.name,
  sirna.name = NULL,
  max.mismatch = 0,
  with.indels = TRUE,
  fixed = TRUE
)

Arguments

target.seq: Pattern to search for in seqs
seqs: The DNAStringSet to be search for instances of the target.seq
seed.name: The seed name to be reported in the data.frame column called seed
sirna.name: Optional siRNA name. A new column called sirna.name will be added to data.frame
max.mismatch: Number of allowed mismatches or the total edit distance
with.indels: If True, include indels
fixed: Require that each sequence symbol matches when searching. Should be FALSE if using wobbles.

Value

A data.frame of matches and ranges for each sequence in seqs

Examples

if (FALSE) { # interactive()

guide.seq = "UUAUAGAGCAAGAACACUGUUUU"

seed.seq = get_seed(guide.seq = guide.seq, seed.name = "mer7m8")

anno.db = load_annotations("rnor7")

SeedMatchR:::.get_match_df(target.seq = seed.seq$Target.Seq,
seqs = anno.db$seqs, seed.name = "mer7m8")
}