annotateOffTargets: annotate off targets

In LihuaJulieZhu/CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

annotate off targets

Description

Annotate Off targets to indicate whether each one (respectively) is inside an exon or intron, as well as 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 TxDb.Celegans.UCSC.ce6.ensGene - for C.elegans
orgAnn	organism annotation mapping such as org.Hs.egSYMBOL. Which lives in the org.Hs.eg.db package for humans.
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

LihuaJulieZhu/CRISPRseek documentation built on Feb. 3, 2024, 2:44 p.m.