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,
      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)

[Package ELMER version 2.12.0 Index]