Outliers removal

[aliciagallego]

Hi again Eric,

Although I have normalized using the function mg$group_coverages(normalization="RPM") I would like to know if there is a way to remove the genes of my region set list that produce outliers and ugly peaks on my metaplots (figure example below).

Thank you in advance.

[ericfournier2]

Hi,

unfortunately, metagene does not have any form of automatic peak/artifact detection. If you want to filter some genes based on their profiles, you have to manually remove them from the regions you pass in.

Cheers,
-Eric

[ericfournier2]

Hi, you can try using the plot_single_region member of the metagene2 object to plot a single region. The function accepts either a region name or a numeric index. Cheers,-Eric Le lundi 15 janvier 2024 à 09 h 52 min 00 s HNE, agallego ***@***.***> a écrit : Hi Eric, Thanks a lot for your response. I have another question but I would not like to saturate the GitHub issue section thus I will ask you here by email. Is there any way of selecting one specific region name with one specific design name to be plotted? In the example below metaplots from all BAM samples (A and B) are computed for all region sets (list 1 and list 2), but I would like to plot A-list1 and B-list2. Is it possible? Thank you. [image: image.png] El lun, 15 ene 2024 a las 15:36, Eric Fournier ***@***.***>) escribió:

Hi, unfortunately, metagene does not have any form of automatic peak/artifact detection. If you want to filter some genes based on their profiles, you have to manually remove them from the regions you pass in. Cheers, -Eric — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AXY4XM4RZCLNEB7QLAK6FETYOU5IPAVCNFSM6AAAAABB3D7DS2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJSGI4TGNRTGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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