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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Changing Fragment object annotation style #1370

Open daccachejoe opened 1 year ago

daccachejoe commented 1 year ago

Hi-

I know this issue has come up in the past when people's data is not annotated in the same way as their annotation objects are and they have had to alter the annotation object via seqlevelsStyle. I encountered an issue combining two datasets who's fragments.tsv.gz files were annotated differently and as such the Fragment object would not align. I ended up working around this by going back and editing the fragments.tsz.gz files of one dataset to match the other but had to do so in linux and re-index the file. If possible, I think it would be incredibly helpful to call a function similar to seqlevelsStyle on the Fragments object and alter the annotation style that way. Not sure if this is something within the package already that I missed though....

Thanks!

timoast commented 1 year ago

Agree, it would be useful and should be possible to convert seqlevel style upon reading from the fragment file, especially in cases where different fragment files use different styles. Ability to set a seqlevelStyle for the object itself will be a longer-term goal as it will take some work to implement.