combineOfftargets: Combine Offtargets

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

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("total.mismatch.bulge", "chromosome", "offTarget_Start",
    "offTarget_End", "offTargetStrand", "offTarget_sequence", "PAM.sequence",
    "guideAlignment2OffTarget", "mismatch.distance2PAM", "n.guide.mismatch",
    "n.PAM.mismatch", "n.DNA.bulge", "n.RNA.bulge", "pos.DNA.bulge", "DNA.bulge",
    "pos.RNA.bulge", "RNA.bulge", "gRNA.name", "gRNAPlusPAM", "predicted_cleavage_score",
    "inExon", "symbol", "entrez_id"),
  exclude.col = "",
  outputFileName,
  comparison.sample1,
  comparison.sample2,
  multiAdjMethod = "BH",
  comparison.score = c("peak_score", "n.distinct.UMIs"),
  overwrite = FALSE
)

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("total.mismatch.bulge","chromosome", "offTarget_Start","offTarget_End", "offTargetStrand","offTarget_sequence","PAM.sequence","guideAlignment2OffTarget", "mismatch.distance2PAM","n.guide.mismatch","n.PAM.mismatch", "n.DNA.bulge","n.RNA.bulge","pos.DNA.bulge","DNA.bulge","pos.RNA.bulge", "RNA.bulge","gRNA.name","gRNAPlusPAM","predicted_cleavage_score", "inExon","symbol","entrez_id")
exclude.col	columns to be excluded before merging. Please check offTargetsInPeakRegions.xls to choose the desired columns to exclude
outputFileName	The merged offtarget file
comparison.sample1	A vector of sample names to be used for comparison. For example, comparison.sample1 = c("A", "B"), comparison.sample2 = rep("Control", 2) indicates that you are interested in comparing sample A vs Control and B vs Control Please make sure the sample names specified in comparison.sample1 and comparison.sample2 are in the sample name list specified in sample.name
comparison.sample2	A vector of sample names to be used for comparison. For example, comparison.sample1 = c("A", "B"), comparison.sample2 = rep("Control", 2) indicates that you are interested in comparing sample A vs Control and B vs Control
multiAdjMethod	A vector of character strings containing the names of the multiple testing procedures for which adjusted p-values are to be computed. This vector should include any of the following: "none", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY", "ABH", and "TSBH". Please type ?multtest::mt.rawp2adjp for details. Default to "BH"
comparison.score	the score to be used for statistical analysis. Two options are available: "peak_score" and "n.distinct.UMIs" n.distinct.UMIs is the number of unique UMIs in the associated peak region without considering the sequence coordinates while peak_score takes into consideration of the sequence coordinates
overwrite	Indicates whether to overwrite the existing file specified by outputFileName, default to FALSE.

Details

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

Value

a data frame containing all off-targets from all samples merged by the columns specified in common.col. 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"),
  comparison.sample1 = c("Cas9Only", "SpCas9-MT3-ZFP"),
  comparison.sample2 = rep("WT-SpCas9", 2),
       outputFileName = "TS2offtargets3Constructs.xlsx")

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