inst/scripts/make-wgbs-data.R

In BIMSBbioinfo/deconvR: Simulation and Deconvolution of Omic Profiles

# Example WGBS data downloaded from ENCODE. It is converted to GRanges format,
# so it can be directly used as example data.
# source from https://www.encodeproject.org/reference-epigenomes/ENCSR527XKV/

# Read the BED methylation calls as methylKit object
wgbs <- methylKit::methRead("ENCFF059FZP.bed",
  sample.id = "sample1", assembly = "hg38",
  header = FALSE, context = "CpG",
  resolution = "base",
  pipeline = list(
    fraction = FALSE,
    chr.col = 1, start.col = 3,
    end.col = 3, coverage.col = 5,
    strand.col = 6, freqC.col = 11
  )
)

# Subset the first 25000 rows
WGBS_GRanges <- methylKit::select(wgbs, 1:25000)

# Convert the raw calls to GRanges and extract methylation values with convertMe
WGBS_GRanges <- deconvR:::convertMe(WGBS_GRanges)

# Save the example data as rda in extdata folder
save(WGBS_GRanges, file = "extdata/WGBS_GRanges.rda")

# Recompress it
tools::resaveRdaFiles("extdata/WGBS_GRanges.rda", "auto")