EpiMix_PlotGene: The EpiMix_PlotGene function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The EpiMix_PlotGene function

Description

plot the genomic coordinate, DM values and chromatin state for each CpG probe of a specific gene.

Usage

EpiMix_PlotGene(
  gene.name,
  EpiMixResults,
  met.platform = "HM450",
  roadmap.epigenome.id = "E002",
  left.gene.margin = 10000,
  right.gene.margin = 10000,
  gene.name.font = 0.7,
  show.probe.name = TRUE,
  probe.name.font = 0.6,
  plot.transcripts = TRUE,
  plot.transcripts.structure = TRUE,
  y.label.font = 0.8,
  y.label.margin = 0.1,
  axis.number.font = 0.5,
  chromatin.label.font = 0.7,
  chromatin.label.margin = 0.02
)

Arguments

gene.name	character string indicating the name of the gene to be plotted.
EpiMixResults	the resulting list object returned from the function of EpiMix.
met.platform	character string indicating the type of the microarray where the DNA methylation data were collected. The value should be either 'HM27', 'HM450' or 'EPIC'. Default: 'HM450'
roadmap.epigenome.id	character string indicating the epigenome id (EID) for a reference tissue or cell type. Default: 'E002'. If the value is empty (""), no histone modifications plot will show.\ Note: Keep this value empty if using the Windows system, since this feature is not supported in Windows.
left.gene.margin	numeric value indicating the number of extra nucleotide bases to be plotted on the left side of the target gene. Default: 10000.
right.gene.margin	numeric value indicating the number of extra nucleotide bases to be plotted on the right side of the target gene. Default: 10000.
gene.name.font	numeric value indicating the font size for the gene name. Default: 0.7.
show.probe.name	logic indicating whether to show the name(s) for each differentially methylated CpG probe. Default: TRUE
probe.name.font	numeric value indicating the font size of the name(s) for the differentially methylated probe(s) in pixels. Default: 0.6.
plot.transcripts	logic indicating whether to plot each individual transcript of the gene. Default: TRUE. If False, the gene will be plotted with a single rectangle, without showing the structure of individual transcripts.
plot.transcripts.structure	logic indicating whether to plot the transcript structure (introns and exons). Non-coding exons are shown in green and the coding exons are shown in red. Default: TRUE.
y.label.font	font size of the y axis label
y.label.margin	distance between y axis label and y axis
axis.number.font	font size of axis ticks and numbers
chromatin.label.font	font size of the labels of the histone proteins
chromatin.label.margin	distance between the histone protein labels and axis

Details

this function requires R package dependencies: karyoploteR, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db

roadmap.epigenome.id: since the chromatin state is tissue or cell-type specific, EpiMix needs to know the reference tissue or cell type in order to retrieve the proper DNase-seq and histone ChIP-seq data. Available epigenome ids can be obtained from the Roadmap Epigenomic study (Nature, PMID: 25693563, figure 2). They can also be retrieved from the list.epigenomes() function.

Value

plot of the genomic coordinate, DM values and chromatin state for each CpG probe of a specific gene.

Examples

library(karyoploteR)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
library(regioneR)

data(Sample_EpiMixResults_Regular)

gene.name = 'CCND2'

roadmap.epigenome.id = 'E096'

EpiMix_PlotGene(gene.name = gene.name,
                EpiMixResults = Sample_EpiMixResults_Regular,
                met.platform = 'HM450',
                roadmap.epigenome.id = roadmap.epigenome.id)

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.