double_flank: Double flank

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

Description

Double flank

Usage

double_flank(
  gr,
  upstart = -200,
  upend = -1,
  downstart = 1,
  downend = 200,
  strandaware = TRUE,
  plot = FALSE,
  linetype_var = "set",
  ...
)

Arguments

gr	GRanges-class
upstart	upstream flank start in relation to start(gr)
upend	upstream flank end in relation to start(gr)
downstart	downstream flank start in relation to end(gr)
downend	downstream flank end in relation to end(gr)
strandaware	TRUE (default) or FALSE
plot	TRUE or FALSE (default)
linetype_var	gr var mapped to linetype
...	passed to plot_intervals

Value

GRanges-class

Examples

# Prime Editing example
#----------------------
    require(magrittr)
    bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38  
    gr <- char_to_granges(c(PRNP = 'chr20:4699600:+',             # snp
                            HBB  = 'chr11:5227002:-',             # snp
                            HEXA = 'chr15:72346580-72346583:-',   # del
                            CFTR = 'chr7:117559593-117559595:+'), # ins
                          bsgenome)
    double_flank(gr, -10,  -1, +1, +20, plot = TRUE)
      
# TFBS example
#-------------
    bedfile  <- system.file('extdata/SRF.bed', package='multicrispr')
    gr  <-  bed_to_granges(bedfile, genome = 'mm10', plot = FALSE)
    double_flank(gr, plot = TRUE)

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.