## ----echo = FALSE, message=FALSE----------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  # comment = "#>", 
  tidy = FALSE, 
  cache = FALSE, 
  results = 'markup'
)

## ----setup, message=FALSE-----------------------------------------------------
suppressWarnings(library(SingleMoleculeFootprinting))
suppressWarnings(library(BSgenome.Mmusculus.UCSC.mm10))

## -----------------------------------------------------------------------------
Methylation = qs::qread(system.file("extdata", "Methylation_4.qs", package="SingleMoleculeFootprinting"))
RegionOfInterest = GRanges("chr6", IRanges(88106000, 88106500))
TFBSs = qs::qread(system.file("extdata", "TFBSs_1.qs", package="SingleMoleculeFootprinting"))

PlotAvgSMF(MethGR = Methylation[[1]], RegionOfInterest = RegionOfInterest, TFBSs = TFBSs)

## -----------------------------------------------------------------------------
MethSM = Methylation[[2]]

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()