Get match results as a column of counts appended to a differential expression results data.frame

Get match results as a column of counts appended to a differential expression results data.frame

Usage

.get_counts_column(
  res,
  target.seq,
  seqs,
  seed.name,
  col.name = NULL,
  shared_genes = TRUE,
  max.mismatch = 0,
  with.indels = F,
  fixed = F
)

Arguments

res: Input differential expression results data.frame
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
col.name: The optional name of the column of match counts. Will default to seed.name if not set
shared_genes: If true, the tx set is reduced to overlapping features in both the sequences db and in the DE data.
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 column of match counts for each gene in res

Examples

if (FALSE) { # interactive()

guide.seq = "UUAUAGAGCAAGAACACUGUUUU"

get_example_data("sirna")

sirna.data = load_example_data("sirna")

res <- sirna.data$Schlegel_2022_Ttr_D1_30mkg

#Load test data
res <- Schlegel_2022_Ttr_D1_30mkg

# Filter results for SeedMatchR
res = filter_res(res, fdr.cutoff=1, fc.cutoff=0, rm.na.log2fc = TRUE)

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

anno.db = load_annotations("rnor7")

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