annotateOffTargets {GUIDEseq} | R Documentation

## Annotate offtargets with gene name

### Description

Annotate offtargets with gene name and whether it is inside an exon

### Usage

    annotateOffTargets(thePeaks, txdb, orgAnn)

### Arguments

`thePeaks` | Output from offTargetAnalysisOfPeakRegions
`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

### Value

A data frame and a tab-delimited file offTargetsInPeakRegions.xls, containing all input offtargets with potential gRNA binding sites, mismatch number and positions, alignment to the input gRNA and predicted cleavage score, and whether the offtargets are inside an exon and associated gene name.

### Author(s)

Lihua Julie Zhu

### See Also

GUIDEseqAnalysis

### Examples

    if (!interactive()) {
        library("BSgenome.Hsapiens.UCSC.hg19")
        library(TxDb.Hsapiens.UCSC.hg19.knownGene)
        library(org.Hs.eg.db)
        peaks <- system.file("extdata", "T2plus100OffTargets.bed",
            package = "CRISPRseek")
        gRNAs <- system.file("extdata", "T2.fa",
            package = "CRISPRseek")
        outputDir = getwd()
        offTargets <- offTargetAnalysisOfPeakRegions(gRNA = gRNAs, peaks = peaks,
            format=c("fasta", "bed"),
            peaks.withHeader = TRUE, BSgenomeName = Hsapiens,
            upstream = 20L, downstream = 20L, PAM.size = 3L, gRNA.size = 20L,
            orderOfftargetsBy = "predicted_cleavage_score",
            PAM = "NGG", PAM.pattern = "(NGG|NAG|NGA)$", max.mismatch = 2L,
            outputDir = outputDir,
            allowed.mismatch.PAM = 3, overwrite = TRUE)
        annotatedOfftargets <- annotateOffTargets(offTargets,
           txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
           orgAnn = org.Hs.egSYMBOL)
    }

[Package GUIDEseq version 1.12.1 Index]