annotateOffTargets: annotate off targets

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

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

CRISPRseek documentation built on Jan. 14, 2021, 2:50 a.m.