annotateOffTargets: Annotate offtargets with gene name

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

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)
}

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.