SeedMatchR_noncanonical_searches

library(SeedMatchR)

Running with wobbles and bulges

wobbles_bulges_matches = run_wobble_bulges_pipeline(guide.seq = guide.seq,
                                                    res =res,features = annodb$seqs,
                                                    bulges_lim = 1)
  
head(wobbles_bulges_matches)

3`-compensatory non-canonical matches

The get_compensatory_sequences function is designed to identify 3’ compensatory sequences for a given siRNA sequence. It takes several parameters, including the guide sequence (guide.seq), seed sequence (seed), a set of DNA sequences (sequences), and various limits and mismatch allowances. The function returns a data frame containing the identified compensatory regions.

comp_matches = get_compensatory_sequences(guide.seq = guide.seq,
                                                seed = get_seed(guide.seq, 'mer7m8')$Target.Seq,
                                                sequences = annodb$seqs,
                                                compensatory_region_length_min = 6,
                                                limit = 100)

head(comp_matches)

comp.list = unique(comp_matches$TX_ID)

# Gene set 2
background.list = res$gene_id[!(res$gene_id %in% comp.list)]

ecdf.results = deseq_fc_ecdf(res, 
                             list("Background" = background.list, 
                                  "Compensetory Matches" = comp.list))

ecdf.results$plot