heatmapGene: Heatmap for correlation between probes DNA methylation and a...

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

This heatmap will sort samples by their gene expression and show the DNA methylation levels of the paired probes to that gene. If no pairs are given, nearest probes will be selected. To use this function you MAE object (input data) will need all probes and not only the distal ones. This plot can be used to evaluate promoter, and intro, exons regions and closer distal probes of a gene to verify if their DNA methylation level is affecting the gene expression

Usage

heatmapGene(
  data,
  group.col,
  group1,
  group2,
  pairs,
  GeneSymbol,
  scatter.plot = FALSE,
  correlation.method = "pearson",
  correlation.table = FALSE,
  annotation.col = NULL,
  met.metadata = NULL,
  exp.metadata = NULL,
  dir.out = ".",
  filter.by.probe.annotation = TRUE,
  numFlankingGenes = 10,
  width = 10,
  height = 10,
  scatter.plot.width = 10,
  scatter.plot.height = 10,
  filename = NULL
)

Arguments

data	A MultiAssayExperiment with a DNA methylation SummarizedExperiment (all probes) and a gene Expression SummarizedExperiment.
group.col	A column from the sample matrix from the MultiAssayExperiment object. Accessed with colData(mae)
group1	A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
group2	A group from group.col. ELMER will run group1 vs group2. That means, if direction is hyper, get probes hypermethylated in group 1 compared to group 2.
pairs	List of probe and pair genes
GeneSymbol	Gene Symbol
scatter.plot	Plot scatter plots
correlation.method	Correlation method: Pearson or sperman
correlation.table	save table with spearman correlation analysis ?
annotation.col	A vector of columns from the sample matrix from the MultiAssayExperiment object. Accessed with colData(mae) to be added as annotation to the heatmap
met.metadata	A vector of metdatada columns available in the DNA methylation GRanges to should be added to the heatmap.
exp.metadata	A vector of metdatada columns available in the Gene expression GRanges to should be added to the heatmap.
dir.out	Where to save the plots
filter.by.probe.annotation	Filter probes to plot based on probes annotation
numFlankingGenes	numFlankingGenes to plot.
width	Figure width
height	Figure height
scatter.plot.width	Scatter plot width
scatter.plot.height	Scatter plot height
filename	File names (.pdf) to save the file (i.e. "plot.pdf"). If NULL return plot.

Value

A heatmap

Author(s)

Tiago Chedraoui Silva (tiagochst at gmail.com)

Examples

## Not run: 
  data <- ELMER:::getdata("elmer.data.example")
  group.col <- "subtype_Expression.Subtype"
  group1 <- "classical"
  group2 <- "secretory"
  pairs <- data.frame(ID = c("cg15924102","cg19403323", "cg22396959"),
                      GeneID = c("ENSG00000196878", "ENSG00000009790", "ENSG00000009790" ),
                      Symbol = c("TRAF3IP3","LAMB3","LAMB3"),
                      Side = c("R1","L1","R3"),
                      Distance = c(6017,168499,0),
                      stringsAsFactors = FALSE)
 heatmapGene(data = data, 
             group.col = group.col,
             group1 = group1, 
             group2 = group2,
             pairs = pairs, 
             GeneSymbol = "LAMB3",
             height = 5,
             annotation.col = c("ethnicity","vital_status"),
             filename = "heatmap.pdf")
 \dontrun{            
     heatmapGene(data = data, 
                 group.col = group.col,
                 group1 = group1, 
                 group2 = group2,
                 GeneSymbol = "ACP6",
                 annotation.col = c("ethnicity","vital_status"),
                 filename = "heatmap_closer_probes.pdf")
 }

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.