Question: Request to remove requirement for gr to have widths 1 in BSseq constructor
0
gravatar for rcavalca
10 months ago by
rcavalca130
United States
rcavalca130 wrote:

Hi,

I'm a big fan of bsseq because it is exactly the data structure I need for a package I maintain (methylSig) that tests for differential methylation (at CpGs and over regions).

As of the Bioc 3.7 release it appears that a check in the BSseq constructor was added (I don't see a reference to it in the NEWS file).

    if(any(width(gr) != 1))
        stop("'gr' needs to have widths of 1")

It was incredibly convenient to be able to create BSseq objects that aggregated CpGs over regions so that there was still a unified methylation object to access and manipulate.

I would like to request that this check be removed to enable BSseq objects with ranges greater than 1bp. Of course, I understand there may be intra-package consistency reasons for the change, but I figured it was worth a shot to ask because I think there is value in BSseq objects that represent methylation over regions.

A quick note, I also posted a GitHub issue because I wasn't sure which got checked faster (https://github.com/hansenlab/bsseq/issues/68)

Thanks, Raymond

bsseq R package • 189 views
ADD COMMENTlink modified 10 months ago by emmascottgm0 • written 10 months ago by rcavalca130
Answer: Request to remove requirement for gr to have widths 1 in BSseq constructor
1
gravatar for Peter Hickey
10 months ago by
Peter Hickey440
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Peter Hickey440 wrote:

That seems a reasonable request, Raymond. Let's continue the discussion on the GitHub issue (I prefer that for more code-focused issues). 

ADD COMMENTlink written 10 months ago by Peter Hickey440
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 186 users visited in the last hour