Running wobble and bulge inclusive seedmatchR pipeline — run_wobble_bulges

This function runs a wobble and bulge inclusive SeedMatchR pipeline.

Usage

run_wobble_bulges_pipeline(
  guide.seq,
  res = res,
  features = features,
  bulges_lim = 4,
  nt = 3,
  silent = FALSE
)

guide.seq: A character string representing the guide sequence.
res: A DESeq2 results data.frame.
features: A DNAStringSet object with sequence information for features. The names of the sequences should be the transcript names.
bulges_lim: An integer representing the number of target bulges allowed per sequence. Default is 4.
nt: An integer representing the length from the start of siRNA where wobbles are not allowed. Default is 3.
silent: A logical value to determine if the function should print progress. Default is FALSE.

A data.frame with the overall matches for each seed.

if (FALSE) { # interactive()
result_df = run_wobble_bulges_pipeline(guide.seq = guide.seq, res = res, features = features)
}