Correlation between gene expression (RNAseq) and RRBS methylation data

Question

[rahel14350]

Dear all,

I have data from gene expression (RNAseq) and RRBS methylation data from mm10. I would like to calculate the Correlation between this data. There are many packages for TCGA data but they didn't work on my data. Do you know any other packages work on RRBS and RNAseq data?

Kind Regards, Rahel

[ATpoint]

they didn't work on my data

What was the problem? Please be more specific.

[rahel14350]

The main reason is that they (for example TCGAvisualize_starburst in TCGAbiolinks or COHCAP package) are for array data such as EPIC, 450K or 27K.

Answer 1

[i.sudbery]

Try inTAD. While this is often used for correlating ATAC-seq with RNA-seq, I think the data in the tutorial is actually methylation data. I certainly don't see any reason it wouldn't work.

[rahel14350]

Well it is not quite the same (if I am correct) because in RRBS we have methylation value for each single site but in ATACseq we have the coverage for each peak region. I might can adapt it by using only the DMRs but then what will be the methylation value for each sample? the mean or median of all sites in the DMRs?

[i.sudbery]

How about taking the DMRs and looking at the average % methylation across them?

[i.sudbery]

How about taking the DMRs and looking at the average % methylation across them?