Blacklist guideRNAs

Source: R/select.R

Adds a blacklist flag to guides not fulfilling defined criteria

selGuides(guideSet, min_Son = NULL, max_Soff = NULL,
  consensus_range = NULL, gc_content = c(0.4, 0.8))

Arguments

min_Son

Numeric. Guides below min_Son are blacklisted. If NULL (the default), min_Son is calculated based on the target score distribution (75th percentile).
max_Soff

Numeric. Guides exceeding min_Son are blacklisted. If NULL (the default), max_Soff is calculated based on the off-target score distribution (99.9th percentile).
consensus_range

Data.frame with repname, start, and end columns. Scores guideRNA target binding sites outside of provided consensus range neutrally.
gc_content

Numeric vector of length two. Elements must be from 0 through 1. For example, c(0.4, 0.8) blacklists guides with GC content not between 40 and 80 percent

Examples

if (FALSE) {
gs <- createGuideSet(Hsapiens, tes = te_annotation_df)
gs <- addTargets(gs, targets = 'LTR13')
gs <- addGuides(gs, guide_length = 16, n_mismatches = 0, gc_content = c(0.25, 0.9), n_clust = 12)
gs <- selGuides(gs, min_Son = 100, gc_content = c(0.1, 0.3))
gs <- plotGuides(gs)
}