search_off_target: Search for candidate off target sequences.

In CicciaLab/iSTOP: iSTOP - Induced STOP Experiment Design

Description

Search for candidate off target sequences allowing for a fixed-band to reduce computation time and a set number of allowed mismatches.

Usage

search_off_target(
  guides,
  genome,
  chromosomes,
  fixed_start = 9,
  fixed_end = 20,
  max_mismatch = 2,
  secondary_filter = NULL,
  cores = 1
)

Arguments

guides	Character vector of sequences to search for fuzzy matches in the genome.
genome	A BSgenome
chromosomes	Character vector of chromosome names to consider when searching the genome.
fixed_start	Beginning of fixed band (no tolerated mismatches). Larger band reduces search time.
fixed_end	End of fixed band (no tolerated mismatches). Larger band reduces search time.
max_mismatch	Number of tolerated mismatches outside of the fixed band.
secondary_filter	A regular expression passed to stringr::str_detect used to filter for off-targets that match this pattern (e.g. 'GG$' will require the matching sequence to end with 'GG').

CicciaLab/iSTOP documentation built on May 9, 2021, 4:55 p.m.