Manhattan_plot: Manhattan plot for all cytosines or regions.

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

Manhattan plot for all cytosines or regions.

Description

This function outputs the Manhattan plot for all cytosines or regions in different chromosomes with significant line based on R package qqman.

Usage

Manhattan_plot(
  siteall_Qvalue,
  chrlabs = NULL,
  col = c("black", "grey"),
  ylab = "-log(Q value)",
  suggestiveline = -log10(0.01),
  genomewideline = -log10(0.001)
)

Arguments

siteall_Qvalue	refers to the input file with Q value from DMR_test(), e.g., regiongeneall_Qvalues, genefeatureall_cpgfeature_Qvalue or others with Q values.
chrlabs	refers to the label of chromosomes, with default NULL.
col	refers to the color of plots, with default black and grey.
suggestiveline	refers to the significant line, with default 0.01.
genomewideline	refers to the genome-wide significant line, with default 0.001.

Value

Outputs a Manhattan figure with Q values.

Examples

Manhattan_plot(siteall_Qvalue, ylab = "-log(Q-value)")
Manhattan_plot(regiongenealls_Qvalue, chrlabs = c(1:18,"X"), col = c("green","orange"), genomewideline = -log10(1e-02))
Manhattan_plot(genefeatureall_cpgfeature_Qvalue, ylab = c("-log(Q value) for CpG island", "-log(Q value) for Shore"), col = c("red","blue"),
suggestiveline = -log10(5e-02), genomewideline = -log10(1e-02))                        

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