Open pcheng84 opened 4 years ago
Thanks for the code, @pcheng84! Yes it would be convenient to have a simplified methylation version pre-computed. @LiNk-NY, it looks like the c("REF", "Chr", "Loc", "Island", "Gene", "UCSC_RefGene_Group")
(and possibly other?) columns would be convenient to have as rowData
and rowRanges
in a RangedSummarizedExperiment
.
Those are the columns I use for the annotation of the islands. I think there are more columns in the listData tables of the IlluminaHumanMethylation450kanno.ilmn12.hg19 annotation object you could add to rowData.
I made a small mistake in my code
lusc <- curatedTCGAData("LUSC", "Methylation_methyl450", FALSE)
should be
mae <- curatedTCGAData("LUSC", "Methylation_methyl450", FALSE)
Hi Phil, @pcheng84
Thank you for pointing this out and providing code to work with.
I think this would be a good addition as an add-on type of package that can optionally replace methylation datasets from curatedTCGAData
.
Currently, it would take me quite some time to re-run the pipeline and integrate the datasets.
It would be easier to have a separate ExperimentHub
package. Let me know what you think.
Thanks!
Best, Marcel
Hi Marcel, @LiNk-NY
An ExperimentHub
package would work nicely. How should we proceed with this?
Cheers, Phil
Hi Phil, @pcheng84 I was thinking we could test-drive functionality that Kayla @kayla-morrell has been working on to make package creation and resource upload easier.
There is a branch called constructHubFunctions
in AnnotationHubData
that lets you run hub_create_package()
. I will look into it as well in the coming days.
https://github.com/Bioconductor/AnnotationHubData/tree/constructHubFunctions
Best, Marcel
Hi Levi and Marcel,
I was wondering if it would be possible to implement a simplified methylation data set. As you know the raw methylation data is quite unwieldy so I condensed it to a matrix, where each row is the median B value for the CpG island. I took the annotation from the IlluminaHumanMethylation450kanno.ilmn12.hg19 library.
here is the code I used to make the simplified methylation values.
Cheers, Phil