buildFeatureVectorForScoringBulge: Build Feature Vector For Scoring Offtargets with Bulge

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

Build Feature Vector For Scoring Offtargets with Bulge

Description

Build Feature Vector For Scoring Offtargets with Bulge

Usage

buildFeatureVectorForScoringBulge(
  alns,
  gRNA.size = 20,
  canonical.PAM = "NGG",
  subPAM.start = 2,
  subPAM.end = 3,
  insertion.symbol = "^",
  PAM.size = 3,
  PAM.location = "3prime"
)

Arguments

alns	alignments, output from getAlnWithBulge (see the example below)
gRNA.size	Size of the gRNA, default to 20L
canonical.PAM	PAM sequence, default to NGG
subPAM.start	start of the subPAM, default to 2L for NGG
subPAM.end	End of the subPAM, default to 3L for NGG
insertion.symbol	Symbol used to indicate bulge in DNA Default to ^
PAM.size	Size of the PAM, default to 3L for NGG
PAM.location	The location of the PAM, default to 3prime

Author(s)

Lihua Julie Zhu

Examples

if (interactive())
{
  library(BSgenome.Hsapiens.UCSC.hg19)
  library(GUIDEseq)
  peaks.f <- system.file("extdata", "T2plus100OffTargets.bed",
     package = "GUIDEseq")
  gRNA <- "GACCCCCTCCACCCCGCCTC"
  temp <- GUIDEseq:::getAlnWithBulge(gRNA, gRNA.name = "T2",
      peaks = peaks.f, BSgenomeName = Hsapiens,
       peaks.withHeader = TRUE)
   fv <- buildFeatureVectorForScoringBulge(temp$aln.indel)
   fv$featureVectors
 }

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