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Shians / NanoMethViz

https://shians.github.io/NanoMethViz/
Apache License 2.0
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filtering option #42

Open selmapichot opened 5 months ago

selmapichot commented 5 months ago

Hi, Could give more details on how and when to use the filtering "options("NanoMethViz.site_filter" = 10L)". I have tried plotting methylation levels with the plot_region function with and without the filtering and they look exactly the same...

Many thanks

Shians commented 5 months ago

This option is use to remove low coverage sites, with your option your data will only contain sites that have at least 10 coverage. If your data is very high coverage, then you don't expect to see a difference in the plots, if you know what coverage your data is at then you can set it to close to that number and see a lot of modification sites removed from the plot. If it doesn't do anything even when set high, then something is wrong with my code and I need to fix it.

The main purpose of the filter is to remove sites that have low coverage, often in modBAM files these are just basecall errors. A filter of 10 is already quite strict, and I would expect it to remove almost all errors.

selmapichot commented 5 months ago

Many thanks for your reply. I have tried increasing the filtering to 30 and it worked. The coverage of the samples is ~40X