annotateOffTargets {CRISPRseek} | R Documentation

## annotate off targets

### Description

annotate off targets to indicate whether it is inside an exon or intron, and the gene id if inside the gene.

### Usage

    annotateOffTargets(scores, txdb, orgAnn, ignore.strand = TRUE)

### Arguments

`scores` | a data frame output from getOfftargetScore or filterOfftarget. It contains strand (strand of the off target, + for plus and - for minus strand), chrom (chromosome of the off target), chromStart (start position of the off target), chromEnd (end position of the off target),name (gRNA name),gRNAPlusPAM (gRNA sequence with PAM sequence concatenated), OffTargetSequence (the genomic sequence of the off target), n.mismatch (number of mismatches between the off target and the gRNA), forViewInUCSC (string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707), score (score of the off target), mismatch.distance2PAM (a comma separated distances of all mismatches to PAM, e.g., 14,11 means one mismatch is 14 bp away from PAM and the other mismatch is 11 bp away from PAM), alignment (alignment between gRNA and off target, e.g., ......G..C.......... means that this off target aligns with gRNA except that G and C are mismatches),NGG (this off target contains canonical PAM or not, 1 for yes and 0 for no) mean.neighbor.distance.mismatch (mean distance between neighboring mismatches)
`txdb` | TxDb object, for creating and using TxDb object, please refer to GenomicFeatures package. For a list of existing TxDb object, please search for annotation package starting with Txdb at http://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData, such as TxDb.Rnorvegicus.UCSC.rn5.refGene for rat, TxDb.Mmusculus.UCSC.mm10.knownGene for mouse, TxDb.Hsapiens.UCSC.hg19.knownGene for human, TxDb.Dmelanogaster.UCSC.dm3.ensGene for Drosophila and TxDb.Celegans.UCSC.ce6.ensGene for C.elegans
`orgAnn` | organism annotation mapping such as org.Hs.egSYMBOL in org.Hs.eg.db package for human
`ignore.strand` | default to TRUE

### Value

a data frame with off target annotation

### Author(s)

Lihua Julie Zhu

### References

Lihua Julie Zhu, Benjamin R. Holmes, Neil Aronin and Michael Brodsky. CRISPRseek: a Bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. Plos One Sept 23rd 2014

### See Also

offTargetAnalysis

### Examples

        library(CRISPRseek)
        #library("BSgenome.Hsapiens.UCSC.hg19")
        library(TxDb.Hsapiens.UCSC.hg19.knownGene)
        library(org.Hs.eg.db)
        hitsFile <-  system.file("extdata", "hits.txt", package="CRISPRseek")
        hits <- read.table(hitsFile, sep = "\t", header = TRUE,
            stringsAsFactors = FALSE)
        featureVectors <- buildFeatureVectorForScoring(hits)
        scores <- getOfftargetScore(featureVectors)
        outputDir <- getwd()
        results <- annotateOffTargets(scores,
            txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
             orgAnn = org.Hs.egSYMBOL)
        results

[Package CRISPRseek version 1.28.0 Index]