Sample_boxplot: Boxplot the methylation levels or read numbers in different...

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

Boxplot the methylation levels or read numbers in different samples.

Description

This function outputs the methylation levels or read numbers of the selected genes or all the genes in the different samples.

Usage

Sample_boxplot(
  inputmethfile,
  inputrefseqfile,
  Meth_plot = TRUE,
  ylab = "Methylation level",
  refseqname = NULL,
  col = NULL
)

Arguments

inputmethfile	refers to the input file with methylation levels.
inputrefseqfile	refers to the input of gene regions.
Meth_plot	refers to whether to plot the methylation levels, with default TRUE, otherwise to plot the read numbers.
ylab	refers to the label of y axis, with default "Methylation level".
refseqname	refers to NCBI ID of specific gene, with default NULL.
col	refers to boxplot colors, with default NULL.

Value

Outputs a boxplot figure with all the samples.

Examples

Sample_boxplot(inputmethfile_QC, inputrefseqfile)
Sample_boxplot(inputmethfile_QC, inputrefseqfile, refseqname = "NM_001011874")
Sample_boxplot(inputmethfile_QC, inputrefseqfile, refseqname = c("NM_001011874", "NM_001289465"))
Sample_boxplot(inputmethfile_QC, inputrefseqfile, ylab = "Methylation level (%)", 
refseqname = c("NM_001011874", "NM_001289465", "NM_008866"), col = c("red", "green", "blue", "yellow", "purple"))

Sample_boxplot(inputmethfile_QC, inputrefseqfile, Meth_plot = FALSE, ylab = "Read number", col = c("red", "blue"))
Sample_boxplot(inputmethfile_QC, inputrefseqfile, Meth_plot = FALSE, ylab = "Read number", refseqname = c("NM_001011874", "NM_001289465"))
Sample_boxplot(inputmethfile_QC, inputrefseqfile, Meth_plot = FALSE, ylab = "Read number", 
refseqname = c("NM_001011874", "NM_001289465", "NM_008866"), col = c("red", "green", "blue"))

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