Cas9

FindsgRNAfunction

R Documentation

sgRNA target design for Shiny App

Description

Warning: This function should not be directly called by the user - it must be called though RunShiny.R

Designs sgRNA based on inputs provided in the Shiny App.

Usage

sgRNA_design_function(userseq, genomename, gtf,
designprogress, userPAM, calloffs, annotateoffs)

Arguments

`userseq`	The target sequence to generate sgRNA guides for. Can either be a character sequence containing DNA bases or the name of a fasta file in the working directory.
`genomename`	The name of a geneome (from the BSgenome package) to check off-targets for.
`gtf`	The name of a genome annotation file (.gtf) in the working directory to check off-target sequences against.
`designprogress`	Assists in communicating the progress of the sgRNA design to the Shiny App.
`userPAM`	An optional argument used to set a custom PAM for the sgRNA. If not set, the function will default to the "NGG" PAM. Warning: Doench efficieny scores are only accurate for the "NGG" PAM.
`calloffs`	If TRUE, the function will search for off-targets in the genome chosen specified by the genomename argument. If FALSE, off-target calling will be skipped.
`annotateoffs`	If TRUE, the function will provide annotations for the off-targets called using the genome annotation file specified by the gtfname argument. If FALSE, off-target annotation will be skipped.

Value

A list containing all data on the generated sgRNA and all off-target information. List items 1 through 15 include information on each individual sgRNA, including the sgRNA sequence itself, PAM, location, direction relative to the target sequence, GC content, homopolymer presence, presence of self-complementarity, off-target matches, predicted efficiency score, and a notes column that summarizes unfavorable sequence features. List items 16 through 27 include all information on off-target matches, including the original sgRNA sequence, off-target sequence, chromosome, location, direction relative to the target sequence, number of mismatches, gene ID, gene name, type of DNA, and exon number.