createBindingFactor.DNA_motif: Create a binding factor object to match a given DNA motif

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

Create a binding factor object to match a given DNA motif

Description

Create a new binding factor based on a DNA motif 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_motif(
  name,
  type = "DNA_motif",
  pwm,
  min.score = "80%",
  with.score = FALSE,
  patternLength = ncol(pwm),
  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,
  verbose = FALSE
)

Arguments

name	give the binding factor a name
type	"DNA_motif" to differentiate from other types
pwm	NULL put motif here as matrix (see biostrings pwm)
min.score	"80%" passed to matchPWM
with.score	FALSE passed to matchPWM
patternLength	length of pattern to be matched [ncol(pwm)]
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]
verbose	set to TRUE for more output

Value

"bindingFactor"

See Also

runLayerBinding createBindingFactor.DNA_regexp

Examples

require(Biostrings)
data(HNF4alpha)    # from Biostrings package
pwm.HNF4A <- PWM(HNF4alpha)  
bf_motif.1 <- createBindingFactor.DNA_motif(name="HNFA_match",pwm = pwm.HNF4A )

bf_motif.2 <- createBindingFactor.DNA_motif(name="HNFA_alter",pwm = pwm.HNF4A ,
                          min.score="80%", with.score=FALSE,
                          profile.layers = NULL,
                          profile.marks=NULL,
                          mod.layers="LAYER.1", mod.marks = 1)

davetgerrard/GenomicLayers documentation built on Nov. 21, 2024, 6:21 a.m.