Regions from subset of CpGs

[Giorgia Migliaccio (TAU)]

Hello!

 

I am using the methylKit package in R to analyze my methylation data.

 

I want to build regions of a subset of CpGs, but I cannot modify methylRawList, that is the input required for the tileMethylCounts.

 

How can I do this?

 

Thanks,

Giorgia

 

Giorgia Migliaccio

PhD Student

FHAIVE

Tampere University

giorgia.mi...@gmail.com

giorgia.m...@tuni.fi

LinkedIn 

 

[Alexander Blume]

Hi Giorgia,

There are multiple ways to subset methylKit objects (see docs). If you want to focus on a particular genomic region, use selectByOverlap(), otherwise you can also subset the single methylRaw objects in a loop and create a new methylRawList via methylRawList(<list of subsetted objects>, treatment=<old treatment>). 

I hope this helps,

Best, 

Alex

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