# 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")
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