Asking about programs and methods to get gene methylation profiles

Question

[Antonio R. Franco]

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

[GenoMax]

https://github.com/shenlab-sinai/ngsplot

deepTools plot profile.

[ATpoint]

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).

Answer 1

[igor]

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

There are also some advanced layout options available: