heatmapPairs: Heatmap of pairs gene and probes anti-correlated

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

Description

Heatmp plot of pairs gene and probes anti-correlated

Usage

heatmapPairs(
  data,
  group.col,
  group1,
  group2,
  pairs,
  subset = FALSE,
  cluster.within.groups = TRUE,
  plot.distNearestTSS = FALSE,
  annotation.col = NULL,
  met.metadata = NULL,
  exp.metadata = NULL,
  width = 10,
  height = 7,
  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
subset	Subset MAE object to keep only groups compared ?
cluster.within.groups	Cluster columns based on the groups
plot.distNearestTSS	Plot track with distNearestTSS ?
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.
width	Figure width
height	Figure 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(Probe = c("cg15924102","cg19403323", "cg22396959"),
                      GeneID = c("ENSG00000196878", "ENSG00000009790", "ENSG00000009790" ),
                      Symbol = c("TRAF3IP3","LAMB3","LAMB3"),
                      Distance = c(6017,168499,0),
                      Raw.p = c(0.001,0.00001,0.001),
                      Pe = c(0.001,0.00001,0.001))
 heatmapPairs(data = data, group.col = group.col,
              group1 = group1, group2 = group2,
              annotation.col = c("ethnicity","vital_status","age_at_diagnosis"),
              pairs, filename = "heatmap.pdf")
  
## End(Not run)

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