up_flank: Extend or Flank GRanges

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

Description

Returns extensions, upstream flanks, or downstream flanks

Usage

up_flank(
  gr,
  start = -200,
  end = -1,
  strandaware = TRUE,
  bsgenome = NULL,
  verbose = FALSE,
  plot = FALSE,
  linetype_var = "set",
  ...
)

down_flank(
  gr,
  start = 1,
  end = 200,
  strandaware = TRUE,
  bsgenome = NULL,
  verbose = FALSE,
  plot = FALSE,
  linetype_var = "set",
  ...
)

extend(
  gr,
  start = -22,
  end = 22,
  strandaware = TRUE,
  bsgenome = NULL,
  verbose = FALSE,
  plot = FALSE,
  linetype_var = "set",
  ...
)

Arguments

gr	GRanges-class
start	number or vector (same length as gr): start definition, relative to gr start (up_flank, extend) or gr end (down_flank).
end	number or vector (same length as gr): end definition, relative to gr start (up_flank) or gr end (extend, down_flank).
strandaware	TRUE (default) or FALSE: consider strand information?
bsgenome	NULL (default) or BSgenome-class. Required to update gr$seq if present.
verbose	TRUE or FALSE (default)
plot	TRUE or FALSE (default)
linetype_var	string: gr var mapped to linetype
...	passed to plot_intervals

Details

up_flank returns upstream flanks, in relation to start(gr). down_flank returns downstream flanks, in relation to end(gr). extend returns extensions, in relation to start(gr) and end(gr)

Value

a GRanges-class

Examples

# PE 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 = bsgenome)
gr %>% up_flank( -22,  -1, plot=TRUE)
gr %>% up_flank( c(-10,-20,-30,-40),  -1, plot=TRUE)
gr %>% up_flank( -22,  -1, plot=TRUE, strandaware=FALSE)

gr %>% down_flank(+1, +22, plot=TRUE)
gr %>% down_flank(+1, c(10, 20, 30, 40), plot=TRUE)
gr %>% down_flank(+1, +22, plot=TRUE, strandaware=FALSE)

gr %>% extend(   -10, +20, plot=TRUE)
gr %>% extend(   -10, +20, plot=TRUE, strandaware=FALSE)

# TFBS example
#-------------
    bedfile <- system.file('extdata/SRF.bed', package='multicrispr')
    gr <- bed_to_granges(bedfile, genome = 'mm10')
    gr %>% extend(plot = TRUE)
    gr %>% up_flank(plot = TRUE)
    gr %>% down_flank(plot = TRUE)

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