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Asking about programs and methods to get gene methylation profiles

Can you gently provide me with programs and methods to get gene methylation profiles such as the image shown below enter image description here

methylation profiles
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updated by igor igor • written by Antonio R. Franco Antonio R. Franco

I guess that this is custom code. Given that you have methylation calls for individual CpGs, you might bin the gene into fractions of, say 0.01 so 1%-wise, and then average the methylation status of the CpGs per bin (be it binary - met or unmet, or averaging the methylation percentage per CpG). I would probably implement this using the R GenomicRanges and use its intersection functions for the downstream. Keep in mind that genes have extreme differences in length, ranging from like 3kb (CEBPA) over like 38kb (UBXN11) or 101kb (VOPP1) to up to 2Mb (DMD), so the question is how informative a plot like this is, especially because no information about the variances are provided (the last sentence is just thinking aloud).

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written by ATpoint ATpoint

1 answer

You can try EnrichedHeatmap. There even some methylation-specific examples in the vignette.

enter image description here

There are also some advanced layout options available:

enter image description here

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written by igor igor

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