heatmapPairs {ELMER}R Documentation

Heatmap of pairs gene and probes anti-correlated

Description

Heatmp plot of pairs gene and probes anti-correlated

Usage

heatmapPairs(data, group.col, group1, group2, pairs, annotation.col = NULL,
  width = 10, height = 10, filename = NULL)

Arguments

data

A MultiAssayExperiment with a DNA methylation martrix or a DNA methylation matrix

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

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

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)

[Package ELMER version 2.2.7 Index]