Genebody_cpgfeature_boxplot: Boxplot the methylation levels for gene body based on CpG...

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

Boxplot the methylation levels for gene body based on CpG island features.

Description

This function outputs the methylation levels in boxplot for one or more features of gene body based on CpG island features, e.g., CpG island and CpG island shore features.

Usage

Genebody_cpgfeature_boxplot(
  genefeatureall_cpgfeature,
  genebodyname = c("promoters", "exons", "introns", "TSSes"),
  ttest = TRUE,
  cpgfeaturelable = c("CpGisland", "Shore"),
  title = c("Promoter", "Exon", "Intron", "TSS"),
  col = NULL
)

Arguments

genefeatureall_cpgfeature	refers to the input file of methylation levels with gene body and CpG island features.
genebodyname	refers to the name of gene body features e.g., promoter, exon, intron and TSSes, with default "promoters", "exons", "introns", "TSSes".
ttest	refers to whether perform the Student t-test, with default TRUE.
cpgfeaturelable	refers to CpG island features, with default "CpGisland" and "Shore".
title	refers to the figure title, with default "Promoter", "Exon", "Intron" and "TSS".
col	refers to the boxplot colors, with default NULL.

Value

Outputs a boxplot figure with gene body and CpG island features.

Examples

Genebody_cpgfeature_boxplot(genefeatureall_cpgfeature)
Genebody_cpgfeature_boxplot(genefeatureall_cpgfeature, genebodyname = c("promoters","exons"), 
ttest = TRUE, cpgfeaturelable = c("CpGisland", "Shore"), title = c("Promoter", "Exon"), col = c("blue", "red"))

Genebody_cpgfeature_boxplot(genefeatureall_cpgfeature, genebodyname = c("promoters","exons","introns","TSSes"), 
ttest = TRUE, cpgfeaturelable = c("CpGisland", "Shore"), title = c("Promoters", "Exons", "Introns", "TSSes"), col = c("blue", "red", "green", "purple"))

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