addCombinations: Add guideRNA combinations to guideSet object.
In tanaylab/repguide: Design CRISPR guide RNAs against DNA repetitive sequences

Description Usage Arguments Value See Also Examples

Finds the optimal combination of non-redundant guideRNAs.

addCombinations(
  guideSet,
  max_guides = 5,
  greedy = TRUE,
  iterations = 10,
  alpha = 100,
  force = FALSE
)

`max_guides`	Numeric. Maximum number of distinct guides to consider when calculating combinations. Do not use a higher number than experimentally feasible.
`greedy`	Logical. If `TRUE` (the default), performs an additional greedy search optimization for selected guide combinations.
`iterations`	Integer > 0. Number of greedy search iterations (10 by default).
`alpha`	Numeric. Off-target score coefficient. Large `alpha` penalizes combinations with high off-target score while `alpha = 0` ignores off-targets and picks combinations with highest on-target binding. Defaults to 10.
`force`	Logical. If `TRUE`, overwrites existing combinations.
`guideSet.`	guideSet object containing guides.
`method`	String. Method of how to pick the best guideRNA per cluster.
`coeff`	Integer. If `method` is `regression`, `coeff` modifies the slope of the linear regression.

Returns a guideSet object contaning combinations.

plotCombinations(), createGuideSet(), addTargets(), and addGuides()

## Not run: 
gs <- createGuideSet(Hsapiens, tes = te_annotation_df)
gs <- addTargets(gs, targets = 'LTR13A')
gs <- addGuides(gs, guide_length = 16)
gs <- addCombinations(gs, max_guides = 8)
gs <- plotCombinations(gs)

## End(Not run)