Annotate offtargets with gene name

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Description

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

Usage

1
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

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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)
}