read_methylome is a function to import methylation data into
a GRanges object. Bed file should be in EPP, ALLC or BisSNP format.
Usage
read_methylome(filename, type, cov_threshold = 1)
Arguments
- filename
filename which contains methylation data
- type
Type of file format. Currently supported epp, bissnp,
bismarkCytosine, bismarkcov, allc and encode
- cov_threshold
numeric, coverage threshold to filter out low coverage
sites, default is 1
Value
a GenomicRange object with methylation, coverage information
Examples
# Read bissnp file
bissnp_path <- system.file(
"extdata",
"bissnp.tsv.gz",
package = "methylTFR"
)
bissnp <- read_methylome(bissnp_path, "bissnp")