DNA Methylome and RNA-seq intersect
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Entering edit mode
20 months ago
Morris_Chair ▴ 330

Hello everyone, I have a methylome dataset and a RNA-seq dataset and I want intersect each other in order to define the methylation status of differentially expressed genes of my interest.

To define the promoter region of all genes in the genome I used this code:

allproms <- promoters(TxDb.Hsapiens.UCSC.hg38.knownGene, downstream = 0, upstream = 2584)


but I’m not sure about the range to give to extract the informations,

My objective is to find out which promoters have methylated bases within their range. I am attempting to do this with the following lines of code:

library(plyranges)
metproms <- join_overlap_inner(allproms, metdat)


Where allproms is the object containing the coordinates and ranges of the promoters, and metdat the object with the ranges for the methylated bases.

Is there a better way to do that?

Thank you

RNA-seq Methylome DNA • 434 views
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Entering edit mode
20 months ago
Tian ▴ 50

Based on my shallow experience, you may try:

• FEM, which statistically integrates: RNA-seq, Methylation, and PPI network.
• MOFA: Multi-Omics Factor Analysis. I used it for multi-omic clustering only.

I will encounter this problem like you soon in next month, so I am also looking for better tools or pure algorithms.