ELMER
  • Introduction
  • Data input
  • Analysis
    • Analysis steps
    • 1 - Creating MAE with distal probes (data input)
    • 2 - Identifying differentially methylated probes
    • 3 - Identifying putative probe-gene pairs
    • 4 - Motif enrichment analysis on the selected probes
    • 5 - Identifying regulatory TFs
    • Compact version with TCGA data
    • TCGA pipe
  • Plots
    • Plot functions
    • 1 - Scatter plots
    • 2 - Schematic plots
    • 3 - Motif enrichment plots
    • 4 - Regulatory TF plots
    • 5 - Heatmap plots
  • Graphical User interface
  • Use case
    • ELMER package
    • Github
    • Bioconductor
    • ELMER.data package
    • Github
    • Bioconductor
    • Bioc2017 workshop
    • Github ELMER/TCGAbiolinks
    • TCGAbiolinks package
    • Github
    • Bioconductor
    • Cedars-sinai
    • center4bfg
    • center4bfg.org
    • University of São Paulo (USP)
    • fmrp.usp.br
    • Fundings
    • FAPESP (16/10436-9)
    • NCI ITCR program (1U01CA184826)
    • Genomic Data Analysis Network NIH/NCI (1U24CA210969)

4.5 - Heatmap plots


Loading required data for plot

# Load results from previous sections
mae <- get(load("mae.rda"))

Heatmap

Generate a heatmap of paired probes.

pair <- read.csv("result/getPair.hypo.pairs.significant.csv")

heatmapPairs(data = mae, 
             group.col = "definition",
             group1 = "Primary solid Tumor", 
             annotation.col = c("years_smoked","gender"),
             group2 = "Solid Tissue Normal",
             pairs = pair,
             filename =  NULL)