getOfftargetScore: Calculate score for each off target

Description

Calculate score for each off target with given feature vectors and weights vector

Usage

getOfftargetScore(featureVectors,  weights = c(0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508,  0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583))

Arguments

featureVectors

a data frame generated from buildFeatureVectorForScoring. It contains IsMismatch.posX (Indicator variable indicating whether this position X is mismatch or not, 1 means yes and 0 means not, X = 1- gRNA.size) representing all positions in the gRNA), 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)

weights

a numeric vector size of gRNA length, default c(0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804, 0.685, 0.583) which is used in Hsu et al., 2013 cited in the reference section

Value

a data frame containing strand (strand of the match, + 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)

Details

score is calculated using the weights and algorithm by Hsu et al., 2013 cited in the reference section

References

Patrick D Hsu, David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, Gang Bao & Feng Zhang (2013) DNA targeting specificity of rNA-guided Cas9 nucleases. Nature Biotechnology 31:827-834

Examples

Run this code

    hitsFile <-  system.file("extdata", "hits.txt", 
        package = "CRISPRseek")
    hits <- read.table(hitsFile, sep = "\t", header = TRUE,
        stringsAsFactors = FALSE)
    featureVectors <- buildFeatureVectorForScoring(hits)
    getOfftargetScore(featureVectors)

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