Quick_DMCs: Quick use the GeneDMRs package for differentially methylated...

In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis

Quick use the GeneDMRs package for differentially methylated cytosine sites.

Description

This function outputs the differentially methylated cytosine sites (DMCs).

Usage

Quick_DMCs(
  paths = paste(system.file(package = "GeneDMRs"), "/methdata", sep = ""),
  suffixmeth = ".gz",
  control_paths = NULL,
  case_paths = NULL
)

Arguments

paths	refers to the path of input file, with default the package path.
suffixmeth	refers to the suffix of methylation file, e.g., ".gz", ".zip" and so on (some files are in text .txt format, then ".txt" or ".txt.gz"), with default ".gz".
control_paths	refers to the path of control groups, with default NULL.
case_paths	refers to the path of case groups, with default NULL.

Value

Outputs DMC results.

Examples

allDMCs <- Quick_DMCs()

# if only case and control group (n = 2) paths are provided #
controls <- c("C:/Users/GeneDMRs/methdata/1_1.gz", "C:/Users/GeneDMRs/methdata/1_2.gz", "C:/Users/GeneDMRs/methdata/1_3.gz")
cases <- c("C:/Users/GeneDMRs/methdata/2_1.gz", "C:/Users/GeneDMRs/methdata/2_1.gz")
allDMCs <- Quick_DMCs(control_paths = controls, case_paths = cases)

xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.