Generating TSS heatmap using methylation data

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2.4 years ago

Minsun • 0

I am trying to generate a TSS heatmap (ex. figure below) using my methylation data derived from WGBS.

enter image description here

I saw many packages for ChIP-seq data such as EnrichedHeatmap but I was having difficulties using those packages since my input data is not ChIP-seq data. My data frame consists of methylation ratio (range: 0-1) for each sample (column) for each CpG site (rows). I am able to map each CpG site to genes and get the distance to TSS using my own method. My example data frame looks something like this.

colnames(df)

"Chromosome" "TSS.start" "TSS.end" "Distance.to.TSS" "Gene.Symbol" "CpG.Start" "CpG.End" "Sample 1" "Sample 2" "Sample 3"

enter image description here

I am wanting to use heatmap.2 in R to generate the TSS heatmap to see if there is an enrichment of methylation near the TSS. Does anyone have suggestion on how I could create a heatmap for non ChIP-seq data?

Thanks!

wgbs r tss methylation heatmap • 622 views

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