#
#Description: Run BayMeth analysis with calcSssI for Control data
#  Sample of Interest sourced from: http://imlspenticton.uzh.ch/robinson_lab/BayMeth/riebler-etal-2014-imr90.zip
#
#  calcSssI table generated for chr7 (hg18), 100bp non-overlapping windows, read length assumed = 300bp
#

library(Repitools)
library(GenomicRanges)

load("calcSssI_with_BayMeth_data.RData")

calc_control <- as.matrix(as.integer(calcSssI_table$lambda))

bml_simSssI <- BayMethList(windows=windows, control=calc_control, sampleInterest=sample_of_interest, cpgDens=cpgdens)

#Proceed with recommended BayMeth analysis steps from Riebler et al. (2014)