read_methylation_report: Read a methylation report file

In geneprophet/BSDMR: a region-based method for quantitating the conservation and divergence of methylation patterns between species by high order features

Description

read_methylation_report read a file containing methylation information using readr. In general, the metyylation report file was generated by Bismark methylation extractor. The methylation report file format is the following: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context> Note: the 7th column is optional.

Usage

read_methylation_report(file, min_coverage = 4, type = "CG")

Arguments

file	the path of methylation report file
min_coverage	filter out the sites which total reads < min_coverage. the default is 4.
type	specify the methylation context type : "CG", "CHG" or "CHH",the default is "CG".

Value

A GRanges object. The GRanges object contains three additional metadata columns:

• methylated_reads: the number if methylated reads for each C sites.

• total_reads: Total number of reads for each C sites.

• type:the C-context type: CG,CHG, or CHH

Author(s)

Hongen Kang [e-mail]

Examples

# Obtain the path to files
## Not run: 
#' file <- system.file("extdata", "example_human_chr22_CpG_report.txt", package = "BSDMR")
human_met <- read_methylation_report(file,min_coverage=4)
file <- system.file("extdata", "example_mouse_chr15_CpG_report.txt", package = "BSDMR")
mouse_met <- read_methylation_report(file,min_coverage=4)

## End(Not run)

geneprophet/BSDMR documentation built on March 3, 2021, 5:50 a.m.