read_met: Read methylation file
In BPRMeth: Model higher-order methylation profiles

Description Usage Arguments Value Important Author(s) See Also Examples

read_met reads a file containing methylation data using the fread function. Since there are different technologies, e.g. array, bulk BS-Seq, scBS-Seq, and still there is no standard file format, different options are available, check the Important section below on the file format for each type you choose. If a file format is not availabe, you need to read the file and create a GRanges object, where the data are ordered by chromosome and genomic location.

read_met(
  file,
  type = "sc_seq",
  strand_info = FALSE,
  chr_discarded = NULL,
  min_bulk_cov = 4,
  max_bulk_cov = 1000,
  delimiter = "\t"
)

`file`	File name.
`type`	Type of technology as character. Either "bulk_seq", "sc_seq" or "array". Check the Important section below for more details.
`strand_info`	Logical, whether or not the file contains strand information.
`chr_discarded`	Optional vector with chromosomes to be discarded.
`min_bulk_cov`	Minimum number of reads mapping to each CpG site. Used only for "bulk_seq" and CpGs with less reads will be discarded as noise.
`max_bulk_cov`	Maximum number of reads mapping to each CpG site. Used only for "bulk_seq" and CpGs with less reads will be discarded as noise.
`delimiter`	Delimiter format the columns are splitted. Default is tab.

A GRanges object.

The GRanges object contains one or two additional metadata columns:

met: Methylation level.
- For "array" this is the Beta or M-values
- For "sc_seq" this is either 0 or 1 (unmethylated or methylated)
- For "bulk_seq" this contains the number of methylated reads for each CpG.
total: Total number of reads for each CpG. Present only for "bulk_seq" type.

These columns can be accessed as follows: granges_obj$met

Depending on technology type we assume different file formats.

"array" File format: "chromosome", "start", "strand" (optional), "met" .
"sc_seq" File format: "chromosome", "start", "strand" (optional), "met" . Where "met" should contain only 1s or 0s.
"bulk_seq" File format: "chromosome", "start", "strand" (optional), "met", "total".

By default columns are considered in tab delimited format.

C.A.Kapourani C.A.Kapourani@ed.ac.uk

read_anno, read_expr, create_region_object

# Obtain the path to files
file <- system.file("extdata", "dummy_met.bed", package = "BPRMeth")
met_dt <- read_met(file)

# Extract methylation level
met <- met_dt$met