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read_methylome

Source: R/data_reader.R
read_methylome.Rd

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

Author

Irem Gunduz

Examples

# Read bissnp file
bissnp_path <- system.file("extdata",
    "bissnp.tsv.gz",
    package = "methylTFR"
)
bissnp <- read_methylome(bissnp_path, "bissnp")