plotMotifFootprint

Creates a footprint plot of bias corrected methylation for a given motif and sample

Usage

plotMotifFootprint(
  motif,
  tf_bindsites,
  msites,
  sample_name = NULL,
  gc_dist,
  gcfreqs,
  enhancer = NULL,
  method = "division",
  flankNorm = 50
)

Arguments

motif

Motif name as a character string

tf_bindsites

Transcript Factor binding sites from the annotation package

msites

Methylation sites as a data frame

sample_name

Optional sample name as a character string, defaults to the file name if not provided

gc_dist

a GRanges object contains Genome wide GC distribution

gcfreqs

GC frequency of the genome used to compute expected methylation

enhancer

Specific region such as distal motif, proximal motif

method

Method to calculate the difference, either "substraction" or "division"

flankNorm

Numeric value indicating the flank normalization distance, default is 50

Value

A ggplot object of TF footprint difference plot for a single sample

Examples

library(ggplot2)
library(methylTFR)

# Load the data
load(system.file("extdata",
    "BATF_tf_bindsites.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "example_data.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "BATF_gcfreqs.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "gcdist_subset.rda",
    package = "methylTFR"
))

# Plot the expected footprint
p <- plotMotifFootprint(
    motif = "BATF",
    tf_bindsites = tf_bindsites,
    msites = msites,
    sample_name = "Sample1",
    gc_dist = gcdist,
    gcfreqs = gcfreqs,
    enhancer = NULL,
    method = "division"
)