search_off_target: Search for candidate off target sequences.

Description Usage Arguments

View source: R/search-off-target.R

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
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.