plot.factorSet: Plot to visualise a set of binding factor profiles and mod...

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

Plot to visualise a set of binding factor profiles and mod layers

Description

show the profile and modification specificities for a set of binding factors.

Usage

## S3 method for class 'factorSet'
plot(factorSet)

Arguments

factorSet

the list of binding factors.

See Also

createBindingFactor.DNA_motif print.bfSet

Examples

testFactor2 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA")

testFactor3 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA", profile.layers = c("LAYER.1", "LAYER.3"), profile.marks = c(0,0), 
                                             mod.layers = c("LAYER.2", "LAYER.4"), mod.marks=c(0,1))

# check that a profile looking for 1 will not find any.  N.B this WILL bind AFTER testFactor2
testFactor4 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA", profile.layers = c("LAYER.3", "LAYER.4"), profile.marks = c(0,1), 
                                             mod.layers = c("LAYER.1", "LAYER.2"), mod.marks=c(0,1))

testFactor5 <- createBindingFactor.layer_region("test5", patternLength = 150)
# now can match things genome wide. Need to run layerBinding and modification.

# need to have a factorSet, a list of bindingFactors

testFS <- list(testFactor2=testFactor2, testFactor3=testFactor3, testFactor4=testFactor4, testFactor5=testFactor5)

plot.factorSet(testFS)

davetgerrard/GenomicLayers documentation built on April 28, 2024, 2:53 p.m.