get_compensatory_sequences — get_compensatory

Function to get 3' compensatory sequences for a given siRNA sequence.

Usage

get_compensatory_sequences(
  guide.seq,
  seed,
  sequences,
  compensatory_region_length_min = 6,
  compensatory_region_length_max = NA,
  limit = 100,
  mismatch_ = 1,
  mismatch_compensatory_region_ = 0
)

Arguments

guide.seq: A character string representing the guide sequence.
seed: A character string representing the seed sequence.
sequences: A DNAStringSet object containing the sequences of the transcripts.
compensatory_region_length_min: An integer representing the minimum length of the compensatory region.
compensatory_region_length_max: An integer representing the maximum length of the compensatory region.
limit: An integer representing the limit for sequence update.
mismatch_: An integer representing the maximum number of mismatches allowed in the seed match.
mismatch_compensatory_region_: An integer representing the maximum number of mismatches allowed in the compensatory region.

Value

A data frame containing the compensatory regions.

Examples

if (FALSE) { # interactive()
}