Quick_GeneDMRs: Quick use the GeneDMRs package for gene based differentially...

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

Quick use the GeneDMRs package for gene based differentially methlated regions.

Description

This function outputs a series of results and figures for gene based regions' methylation analysis.

Usage

Quick_GeneDMRs(
  paths = paste(system.file(package = "GeneDMRs"), "/methdata", sep = ""),
  suffixmeth = ".gz",
  control_paths = NULL,
  case_paths = NULL,
  bedfile = "refseq",
  suffixbed = ".txt",
  Dbannotation = "org.Mm.eg.db",
  keggorganism = "mmu"
)

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.
bedfile	refers to the file name of bed file for "refseq". This file is downloaded from UCSC website, with default "refseq".
suffixbed	refers to the suffix of bed file, e.g., ".gz", ".zip" and so on (some files are in text .txt format, then ".txt" or ".txt.gz"), with default ".txt".
Dbannotation	refers to the annotation dataset for enrichment, with default "org.Mm.eg.db" of mouse.
keggorganism	refers to the species name for KEGG enrichment, with default "mmu" of mouse.

Value

Outputs a series of DMG results.

Examples

allDMGs <- Quick_GeneDMRs()
allDMGs_mouse <- Quick_GeneDMRs(Dbannotation = "org.Mm.eg.db", keggorganism = "mmu")

# 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")
allDMGs <- Quick_GeneDMRs(paths = "C:/Users/GeneDMRs/methdata", control_paths = controls, case_paths = cases)

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