MEDIPS.CpGenrich now that RangedData is deprecated
1
0
Entering edit mode
emham • 0
@emham-23009
Last seen 4.1 years ago

Hi all,

I've been trying to use the MEDIPS.CpGenrich function in the MEDIPS package (with R 3.6 and BioC 3.10), which throws an error because it uses RangedData objects which are now deprecated. Has anyone either found a workaround to this or modified the MEDIPS.CpGenrich code to migrate it to GRanges?

Thanks!

MEDIPS RangedData GenomicRanges • 702 views
ADD COMMENT
1
Entering edit mode
Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 6.1 years ago
USA/La Jolla/UCSD

Dear Emily,

Thank you for your email!

Unfortunately the MEDIPS.CpGenrich() function depends on RangedData, which is not available any more. I have not updated MEDIPS to function without RangedData and will not be able to do so in the near future. Therefore, MEDIPS.CpGenrich() is not available for the time being unless you manage to find an old R/Bioconductor setting where RangedData are still available.

I also would like to stress that we have developed a new package ‘qsea’, which has a much improved method for estimating %methylation from MeDIP-seq data. It also does not have the CG enrichment QC, but is much more flexible in terms of parameter settings etc.

Best wishes, Lukas

ADD COMMENT

Login before adding your answer.

Traffic: 891 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6