getofftargetdata {crispRdesignR} | R Documentation |
Off Target Data Frame Creation
Description
Will provide a data frame with all information about the generated sgRNA returned by the sgRNA_design function.
Usage
getofftargetdata(x)
Arguments
x |
the data list generated by the sgRNA_design function |
Value
A data frame containing all information on potential off-target sequences generated by the sgRNA_design function. Information includes 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
Examples
## Quick example without off-target searching or annotation
## First generate data with the sgRNA_Design Function
testseq <- "GGCAGAGCTTCGTATGTCGGCGATTCATCTCAAGTAGAAGATCCTGGTGCAGTAGG"
usergenome <- "placeholder"
gtfname <- "placeholder"
alldata <- sgRNA_design(testseq, usergenome, gtfname, calloffs = FALSE)
## Then separate and format the off-target data with getofftargetdata()
final_data <- getofftargetdata(alldata)
## Longer example with off-target searching and annotation
## First generate data with the sgRNA_Design Function
requireNamespace("BSgenome.Scerevisiae.UCSC.sacCer3", quietly = TRUE)
testseq <- "GGCAGAGCTTCGTATGTCGGCGATTCATCTCAAGTAGAAGATCCTGGTGCAGTAGG"
usergenome <- BSgenome.Scerevisiae.UCSC.sacCer3::BSgenome.Scerevisiae.UCSC.sacCer3
gtfname <- "Saccharomyces_cerevisiae.R64-1-1.92.gtf.gz"
annotation_file <- system.file("example_data", gtfname, package = "crispRdesignR")
alldata <- sgRNA_design(testseq, usergenome, annotation_file)
## Then separate and format the sgRNA data with getofftargetdata()
final_data <- getofftargetdata(alldata)
[Package crispRdesignR version 1.1.7 Index]