MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames?
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@tptacek3050-7477
Last seen 6.4 years ago
United States

I didn't see this in the documentation so I thought I'd ask here.

 

I was wondering whether there was any way to get more data about the merged regions from MEDIPS.mergeFrames. Specifically, I was thinking about pValue, absolute counts, rpkm, and log2FC. I'm assuming that these would be average values ... which would be fine. The researchers I'm working with are just looking for a table that has this information summarized so they can more quickly browse differentially methylated regions.

 

Is this possible, or will I need to write a script to run the calculations myself?

MEDIPS mergeFrames • 739 views
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Lukas Chavez ▴ 570
@lukas-chavez-5781
Last seen 3.7 years ago
USA/La Jolla/UCSD
Dear tptacek3050, the function MEDIPS.mergeFrames() merges the genomic coordinates of preselected significant neighbouring genomic windows with respect to a given maximal distance. While it is in principle possible to calculate averaged values for counts, it is no valid to calculate average p-values. Therefore, the function MEDIPS.mergeFrames() returns genomic coordinates only. There are now two options to obtain summarized information for the obtained merged windows: i) apply the function MEDIPS.selectROIs() by providing the genome wide result table at the slot ‘results' and the merged windows object obtained from MEDIPS.mergeFrames() at the ‘rois’ slot, and setting summarize=“avg". Here, it is recommended to select valid columns like the counts columns only (see also an example in the respective man page). ii) Use the merged genomic windows as regions of interest and run the MEDIPS.createROIset() instead of MEDIPS.createSet(). Afterwards you can do a quantitative coverage comparison between conditions as usual but for the merged windows only. All the best, Lukas > On 05 May 2015, at 17:56, tptacek3050 [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User tptacek3050 wrote Question: MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames?: > > > I didn't see this in the documentation so I thought I'd ask here. > > > I was wondering whether there was any way to get more data about the merged regions from MEDIPS.mergeFrames. Specifically, I was thinking about pValue, absolute counts, rpkm, and log2FC. I'm assuming that these would be average values ... which would be fine. The researchers I'm working with are just looking for a table that has this information summarized so they can more quickly browse differentially methylated regions. > > > Is this possible, or will I need to write a script to run the calculations myself? > > > You may reply via email or visit MEDIPS: Any way to get more columns/data from MEDIPS.mergeFrames? >
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I decided to go ahead and write a bash script to compile the data. I also went with minimum p-value instead of averaging (I know its not valid ... we were just looking for a way to attach some measure of significance to the merged interval).

 

Thanks for the feedback anyway. I may try using the methods you posted in the future.

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