Skip to contents

Search input Biostrings::DNAStringSet for a set of defined sequences

full_search_ranges.Rd

This function will use Biostrings::vcountpattern to find matches to the input siRNA sequence. This function will then provide a matrix that is sequences x match type. The best match will be reported based on a pre-defined list of rankings.

Usage

full_search_ranges(
  guide.seq,
  seqs,
  group.name = "siRNA",
  indel.bool.opt = c(TRUE, FALSE),
  edit.dist.list = c(0:4),
  seqs.to.search = c("Full", "18mer", "15mer", "mer8", "mer7m8", "mer7A1", "mer6"),
  fixed.opt = FALSE,
  max.seed.edit.dist = 1
)

Arguments

guide.seq

Input guide sequence

seqs

Biostrings::DNAStringSet of sequences to search

group.name

Group name to use for labeling

indel.bool.opt

Vector of indel options.

edit.dist.list

A vector of possible edit distances.

List of sequences to search. Options: "Full", "18mer", "mer8", "mer7m8", "mer7A1", "mer6"

fixed.opt

A vector of possible fixed paramters.

max.seed.edit.dist

An integer value indicating allowed edit distance for seed searches.

Value

A data.frame of sequence match counts

Examples

if (FALSE) { # interactive()
print("TBD")
}