createBindingFactor.DNA_regexp: Create a binding factor object to match a given pattern of...

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

Create a binding factor object to match a given pattern of layers

Description

Create a new binding factor based on a simple pattern of marks on others layers and may (when used) set marks on other layers.

Usage

createBindingFactor.DNA_regexp(
  name,
  type = "DNA_regexp",
  forRegExp = "N",
  revRegExp = "N",
  patternLength = 0,
  profile.layers = NULL,
  profile.marks = NULL,
  mod.layers = NULL,
  mod.marks = NULL,
  offset = 0,
  offset.method = NULL,
  offset.params = NULL,
  stateWidth = patternLength,
  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	"DNA_regexp" to differentiate from other types
forRegExp	= regular expression to match DNA sequence
revRegExp	= reverse complement of forRegExp
patternLength	[= 0] an approximate length of match but may not be the actual matched length, which may vary for regular expression matches
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
stateWidth	the width of pattern to recognise on other layers
test.layer0.binding	when creating, test if the DNA sequence has a match.
test.mismatch.rate	proportion of mismatches to tolerate when testing
max.pattern.tries	NA
min.DM.length	NA
verbose	set to TRUE for more output
min.DR.lengt	NA

Value

"hits"

See Also

runLayerBinding createBindingFactor.DNA_motif

Examples

simpleBF <- createBindingFactor.DNA_regexp("test", patternString="ACTGGGCTA")

# this regular expression finds 4 CpGs with 0-4 bases between them
CGI<- createBindingFactor.DNA_regexp("CGI", patternString="(CG.{0,4}){3}CG", 
                          patternLength=20, mod.layers = "CpG_island",
                          mod.marks=1, stateWidth=20)
                          
RAP1 <- createBindingFactor.DNA_regexp("RAP1", forRegExp="GGTGT(.{0,3})GGTGT",
                                    revRegExp="ACACC(.{0,3})ACACC",patternLength=20, 
                                    mod.layers = "RAP1_bound", mod.marks=1, stateWidth=20)                         

davetgerrard/GenomicLayers documentation built on Jan. 12, 2025, 5:06 p.m.