combineOfftargets: Combine Offtargets

Description Usage Arguments Details Value Author(s) Examples

View source: R/combineOfftargets.R

Description

Merge offtargets from different samples

Usage

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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

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    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 May 2, 2018, 2:41 a.m.