Usage
filterOffTarget(scores, min.score = 0.5, topN = 100, topN.OfftargetTotalScore = 10, annotateExon = TRUE, txdb, orgAnn, outputDir, oneFilePergRNA = FALSE, fetchSequence = TRUE, upstream = 200, downstream = 200, BSgenomeName, baseBeforegRNA = 4, baseAfterPAM = 3, featureWeightMatrixFile = system.file("extdata", "DoenchNBT2014.csv",
package = "CRISPRseek"))
Arguments
scores
a data frame output from getOfftargetScore. It contains strand (strand of the
off target, + for plus and - for minus strand), chrom (chromosome of the off
target), chromStart (start position of the off target), chromEnd (end position
of the off target),name (gRNA name),gRNAPlusPAM (gRNA sequence with PAM
sequence concatenated), OffTargetSequence (the genomic sequence of the off
target), n.mismatch (number of mismatches between the off target and the
gRNA), forViewInUCSC (string for viewing in UCSC genome browser, e.g.,
chr14:31665685-31665707), score (score of the off target),
mismatch.distance2PAM (a comma separated distances of all mismatches to
PAM, e.g., 14,11 means one mismatch is 14 bp away from PAM and the other
mismatch is 11 bp away from PAM), alignment (alignment between gRNA and off
target, e.g., ......G..C.......... means that this off target aligns with
gRNA except that G and C are mismatches),NGG (this off target contains
canonical PAM or not, 1 for yes and 0 for no) mean.neighbor.distance.mismatch
(mean distance between neighboring mismatches)
min.score
minimum score of an off target to included in the final output, default 0.5
topN
top N off targets to be included in the final output, default 100
topN.OfftargetTotalScore
top N off target used to calculate the total off target score, default 10
annotateExon
Choose whether or not to indicate whether the off target is inside an exon or
not, default TRUE
txdb
TxDb object, for creating and using TxDb object, please refer
to GenomicFeatures package. For a list of existing TxDb object, please
search for annotation package starting with Txdb at
http://www.bioconductor.org/packages/release/BiocViews.html#___AnnotationData,
such as TxDb.Rnorvegicus.UCSC.rn5.refGene for rat,
TxDb.Mmusculus.UCSC.mm10.knownGene for mouse,
TxDb.Hsapiens.UCSC.hg19.knownGene for human,
TxDb.Dmelanogaster.UCSC.dm3.ensGene for Drosophila and
TxDb.Celegans.UCSC.ce6.ensGene for C.elegans
orgAnn
organism annotation mapping such as org.Hs.egSYMBOL in org.Hs.eg.db package for human
outputDir
the directory where the off target analysis and reports will be written to
oneFilePergRNA
write to one file for each gRNA or not, default to FALSE
fetchSequence
Fetch flank sequence of off target or not, default TRUE
upstream
upstream offset from the off target start, default 200
downstream
downstream offset from the off target end, default 200
BSgenomeName
BSgenome object. Please refer to available.genomes in BSgenome package. For
example, BSgenome.Hsapiens.UCSC.hg19 for hg19, BSgenome.Mmusculus.UCSC.mm10
for mm10, BSgenome.Celegans.UCSC.ce6 for ce6, BSgenome.Rnorvegicus.UCSC.rn5
for rn5, and BSgenome.Dmelanogaster.UCSC.dm3 for dm3
baseBeforegRNA
Number of bases before gRNA used for calculating gRNA efficiency, default 4
baseAfterPAM
Number of bases after PAM used for calculating gRNA efficiency, default 3
featureWeightMatrixFile
Feature weight matrix file used for calculating gRNA efficiency. By default DoenchNBT2014 weight matrix is used. To use alternative weight matrix file, please input a csv file with first column containing significant features and the second column containing the corresponding weights for the features. Please see Doench et al., 2014 for details.