FindsgRNAfunction: sgRNA target design for Shiny App

Description Usage Arguments Value Author(s)

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

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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.

Author(s)

Dylan Beeber


crispRdesignR documentation built on Jan. 13, 2021, 4:46 a.m.