createRandomBindingFactor: Randomly generate a binding factor

In davetgerrard/GenomicLayers: Simple, sequence-based simulation of epi-genomes.

Randomly generate a binding factor

Description

Create a new binding factor that may also require marks on others layers and may (when used) set marks on other layers. Need to specify the type of factor.

Usage

createRandomBindingFactor(
  name,
  layerSet,
  type = c("DNA_motif", "DNA_region", "layer_region", "layer_island"),
  test.layer0.binding = FALSE,
  test.mismatch.rate = 0.1,
  max.pattern.tries = 1000,
  min.DM.length = 2,
  min.DR.length = 10,
  verbose = FALSE
)

Arguments

name	give the binding factor a name
type	[c("DNA_motif", "DNA_region","layer_region","layer_island")] to differentiate from other types
test.layer0.binding	when creating, test if the DNA sequence has a match.
test.mismatch.rate	proportion of mismatches to tolerate when testing [.1]
max.pattern.tries	1000
min.DM.length	2
verbose	set to TRUE for more output
patternString	["N"] put motif here (using IUPAC codes for degenerate bases)
patternLength	length of pattern to be matched [nchar(patternString)]
stateWidth	the width of pattern to recognise on other layers
profile.layers	a vector of named layers to set as a match
profile.marks	a vector of 0/1 to match the layers in profile.layers
mod.layers	a vector of named layers to alter on a match
mod.marks	a vector of 0/1 to set on the mod.layers
min.DR.lengt	10

Value

"bindingFactor"

See Also

runLayerBinding createBindingFactor.DNA_regexp

Examples

rBf <- createRandomBindingFactor(name="DNA_A",type="DNA_motif",patternString = "CAT" )

davetgerrard/GenomicLayers documentation built on April 23, 2024, 3:55 p.m.