createBindingFactor.DNA_consensus: Create a binding factor object to match a given DNA consensus

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

Create a binding factor object to match a given DNA consensus

Description

Create a new binding factor based on a DNA consensus that may also require marks on others layers and may (when used) set marks on other layers. Makes use of biostrings function vmatchPattern Can use IUPAC codes and allow mismatches

Usage

createBindingFactor.DNA_consensus(
  name,
  type = "DNA_consensus",
  patternString = "N",
  patternLength = nchar(patternString),
  stateWidth = patternLength,
  profile.layers = NULL,
  profile.marks = NULL,
  mod.layers = NULL,
  mod.marks = NULL,
  offset = 0,
  offset.method = NULL,
  offset.params = NULL,
  test.layer0.binding = FALSE,
  test.mismatch.rate = 0.1,
  max.pattern.tries = 1000,
  min.DM.length = 2,
  min.DR.length = 10,
  verbose = FALSE,
  max.mismatch = 0,
  min.mismatch = 0,
  with.indels = FALSE,
  fixed = TRUE,
  algorithm = "auto"
)

Arguments

name	give the binding factor a name
type	"DNA_consensus" to differentiate from other types
patternString	"N" put consensus 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
offset	0 integer value to indicate relative distance from pattern to apply modifications. Very simple.
offset.method	NULL a function to apply to apply offset. MUST have parameter "n" that is used internally to represent the number of hits.
offset.params	NULL a list of named parameters to pass to offset.method function
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	NA
min.DM.length	NA
verbose	set to TRUE for more output
max.mismatch	0 see vmatchPattern
min.mismatch	0 see vmatchPattern
with.indels	FALSE see vmatchPattern
fixed	TRUE see vmatchPattern
algorithm	"auto" see vmatchPattern
min.DR.lengt	NA

Value

"bindingFactor"

See Also

runLayerBinding createBindingFactor.DNA_regexp

Examples

DNA_A <- createBindingFactor.DNA_consensus(name="DNA_A",patternString = "CAT" )

gc1-2 <- createBindingFactor.DNA_consensus(name="gc1-2",
                          patternString="SSSSSSSSSSSSSSSS",
                          max.mismatch= 2, 
                          min.mismatch= 1,
                          fixed="subject",
                          profile.layers = NULL,
                          profile.marks=NULL,
                          mod.layers="LAYER.1", mod.marks = 1)

davetgerrard/GenomicLayers documentation built on Sept. 23, 2024, 3:53 p.m.