Add guideRNAs to guideSet object

Source: R/add.R

Computes target guideRNA universe and maps, annotates, and scores their genomic targets.

addGuides(guideSet, guides = NULL, n_mismatches = 0,
  blacklist_penalty = 10, guide_length = 19, gc_content = c(0.4,
  0.8), min_Son = NULL, max_Soff = NULL, consensus_range = NULL,
  alpha = 100, n_clust = 11, five_prime_seq = NULL, PAM = "NGG",
  lower_count = 5, force = FALSE)

Arguments

guides

Character. Optional vector of pre-computed guideRNA sequences to map and annotate. Will restrict downstream analysis to guides rather than computing all possible guides de novo.
n_mismatches

Integer from 0 through 3. Maximal number of tolerated mismatches when assessing guideRNA binding targets. Defaults to 0.
guide_length

Single integer between 12 and 26. Basepair size of the guideRNAs. Defaults to 16.
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. Passed to selGuides().
min_Son

Numeric. Minimal on target score of guides. If NULL (the default), will estimate a value based on the on score distribution. Passed to selGuides().
consensus_range

Data.frame with repname, start, and end columns. Scores guideRNA target binding sites outside of provided consensus range neutrally. Passed to selGuides()
alpha

Numeric. Off-target score coefficient. Large alpha penalizes guides with high off-target score while alpha = 0 ignores off-targets and picks guides with highest on-target binding.
n_clust

Single positive integer <= 20. Number of groups to cluster guideRNAs into. Higher n_clust usually gives better results but comes with a speed penalty when computing guide combinations. Passed to clustGuides().
five_prime_seq

Character. Sequence requirement for 5' start of guideRNAs, e.g. G nucleotide for transcription from U6 promoter.
PAM

Character. Currently only 'NGG' PAM is supported.
lower_count

Numeric. Passed to jellyfish kmer counting. Only kmers occuring at least lower_count times are considered for bowtie mapping.
force

Logical. If TRUE, overwrite existing guides.
guideSet.

guideSet object containing targets.
blacklist_penalty.

Numeric. Off-target score multiplier (10 by default) for blacklisted genomic regions. Ignored if blacklisted(guideSet) is empty.
min_Soff

Numeric. Maximal off target score of guides. If NULL (the default), will estimate a value based on the off score distribution. Passed to selGuides().

Value

Returns a guideSet object containing guides.

See also

plotGuides(), createGuideSet(), addTargets(), addCombinations(), clustGuides(), and selGuides

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 <- plotGuides(gs)
}