combineOfftargets: Combine Offtargets

In GUIDEseq: GUIDE-seq analysis pipeline

Description

Merge offtargets from different samples

Usage

combineOfftargets(offtarget.folder, sample.name, 
    remove.common.offtargets = FALSE,control.sample.name,
    offtarget.filename = "offTargetsInPeakRegions.xls", 
    common.col = c("offTarget","predicted_cleavage_score", 
        "gRNA.name", "gRNAPlusPAM", "offTarget_sequence", 
        "guideAlignment2OffTarget", "offTargetStrand", 
        "mismatch.distance2PAM", "n.PAM.mismatch", 
        "n.guide.mismatch", "PAM.sequence", "offTarget_Start",
         "offTarget_End", "chromosome"),
    exclude.col, 
    outputFileName)

Arguments

offtarget.folder	offtarget summary output folders created in GUIDEseqAnalysis function
sample.name	Sample names to be used as part of the column names in the final output file
remove.common.offtargets	Default to FALSE If set to TRUE, off-targets common to all samples will be removed.
control.sample.name	The name of the control sample for filtering off-targets present in the control sample
offtarget.filename	Default to offTargetsInPeakRegions.xls, generated in GUIDEseqAnalysis function
common.col	common column names used for merge files. Default to c("offTarget","predicted_cleavage_score", "gRNA.name", "gRNAPlusPAM", "offTarget_sequence", "guideAlignment2OffTarget", "offTargetStrand", "mismatch.distance2PAM", "n.PAM.mismatch", "n.guide.mismatch", "PAM.sequence", "offTarget_Start", "offTarget_End", "chromosome")
exclude.col	columns to be excluded before merging. Please check offTargetsInPeakRegions.xls to choose the desired columns to exclude
outputFileName	The merged offtarget file

Details

Please note that by default, merged file will only contain peaks with offtargets found in the genome in GUIDEseqAnalysis function.

Value

a tab-delimited file similar to offTargetsInPeakRegions.tsv, containing all peaks from all samples merged by potential gRNA binding sites, mismatch number and positions, alignment to the input gRNA and predicted cleavage score. Sample specific columns have sample.name concatenated to the original column name, e.g., peak_score becomes sample1.peak_score.

Author(s)

Lihua Julie Zhu

Examples

    offtarget.folder <- system.file("extdata", 
        c("sample1-17", "sample2-18", "sample3-19"),
        package = "GUIDEseq")
    mergedOfftargets <- 
       combineOfftargets(offtarget.folder = offtarget.folder, 
       sample.name = c("cas9Only", "WT SpCas9", "SpCas9-MT3-ZFP"), 
       outputFileName = "TS2offtargets3Constructs.xls")

GUIDEseq documentation built on Nov. 8, 2020, 5:27 p.m.