GUIDEseq (version 1.2.1)

combineOfftargets: Combine Offtargets

Description

Merge offtargets from different samples

Usage

combineOfftargets(offtarget.folder, sample.name,  offtarget.filename = "offTargetsInPeakRegions.xls",  common.col = c("targetSeqName", "chromosome",  "offTargetStrand", "offTarget_Start",  "offTarget_End", "gRNAPlusPAM", "offTarget_sequence", "n.mismatch", "guideAlignment2OffTarget",  "predicted_cleavage_score"),  exclude.col = "name",  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

offtarget.filename

Default to offTargetsInPeakRegions.xls, generated in GUIDEseqAnalysis function

common.col

common column names used for merge files. Default to c("targetSeqName", "chromosome", "offTargetStrand", "offTarget_Start", "offTarget_End", "gRNAPlusPAM", "offTarget_sequence", "n.mismatch", "guideAlignment2OffTarget", "predicted_cleavage_score")

exclude.col

columns to be excluded before merging. Default to name (second column of offTargetsInPeakRegions.xls). Please check offTargetsInPeakRegions.xls to choose the desired columns to exclude

outputFileName

The merged offtarget file

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.

Details

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

Examples

if(interactive())
{
    offtarget.folder 
    sample.name
    outputFileName
    mergedOfftargets <- 
        combineOfftargets(offtarget.folder = offtarget.folder, 
        sample.name = sample.name, 
        outputFileName = outputFileName) 
}