scores
a data frame output from getOfftargetScore or filterOfftarget. 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)
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