MEDIPS.CpGenrich now that RangedData is deprecated
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emham • 0
@emham-23009
Last seen 20 months 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 • 202 views
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Entering edit mode
Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 3.7 years ago
USA/La Jolla/UCSD

Dear Emily,

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

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