addTargets: Add targets to a guideSet object

In tanaylab/repguide: Design CRISPR guide RNAs against DNA repetitive sequences

Description

Add targets to a guideSet object

Usage

addTargets(guideSet, targets = NULL, force = FALSE)

Arguments

guideSet	guideSet object containing genome annotation.
targets	Character vector of family identifiers or GRanges object with coordinates and 'repname' metacolumn.
force	Logical. If TRUE, overwrites existing results.

Value

Returns a guideSet object containing targets.

See Also

plotTargets(), and GenomicRanges::makeGRangesFromDataFrame()

Examples

## Not run: 
gs <- createGuideSet(Hsapiens, tes = te_anno)

# Use family identifiers as targets
gs <- addTargets(guideSet, targets = c('LTR12C', 'LTR12E'))

# Use custom regions as targets
target_coords <- GenomicRanges::makeGRangesFromDataFrame(data.frame('chrom'   = c('chr1', 'chr4'), 
                                                                    'start'   = c(1000, 10020),
                                                                    'end'     = c(1122, 10090),
                                                                    'strand'  = c('+', '-'),
                                                                    'repname' = c('ImaginativeTE', 'ImaginativeTE'),
                                                                    'te_id'  = c(1:2)),
                                                         keep.extra.columns = TRUE)
gs <- addTargets(guideSet, targets = target_coords)

## End(Not run)

tanaylab/repguide documentation built on June 29, 2020, 9:29 a.m.