buildFeatureVectorForScoring: Build feature vectors

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

Build feature vectors

Description

Build feature vectors for calculating scores of off targets

Usage

buildFeatureVectorForScoring(
  hits,
  gRNA.size = 20,
  canonical.PAM = "NGG",
  subPAM.position = c(22, 23),
  PAM.size = 3,
  PAM.location = "3prime"
)

Arguments

hits	A Data frame generated from searchHits, which contains IsMismatch.posX - Indicator variable indicating whether this position X is mismatch or not, (1 means yes and 0 means not). X takes on values from 1 to gRNA.size, representing all positions in the guide RNA (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 - Set to 100, and will be calculated in getOfftargetScore
gRNA.size	gRNA size. The default is 20
canonical.PAM	Canonical PAM. The default is NGG for spCas9, TTTN for Cpf1
subPAM.position	The start and end positions of the sub PAM to fetch. Default to 22 and 23 for SP with 20bp gRNA and NGG as preferred PAM
PAM.size	Size of PAM, default to 3 for spCas9, 4 for Cpf1
PAM.location	PAM location relative to gRNA. For example, default to 3prime for spCas9 PAM. Please set to 5prime for cpf1 PAM since it's PAM is located on the 5 prime end

Value

A data frame with hits plus features used for calculating scores and for generating report, including

• 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

• mismatche.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

Author(s)

Lihua Julie Zhu

See Also

offTargetAnalysis

Examples

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

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