combineOfftargets {GUIDEseq} | R Documentation

## Combine Offtargets

### 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")

[Package GUIDEseq version 1.14.0 Index]