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MissionBio / mosaic

Tertiary analysis package to visualize single-cell data generated by the Tapestri Platform.
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By what criteria does the load function filter dna variants? #16

Closed msteph11 closed 1 year ago

msteph11 commented 1 year ago

Hello,

I've been using the apply_filter option for the load function (https://missionbio.github.io/mosaic/pages/functions/missionbio.mosaic.io.load.html), as the resulting object is too big otherwise. I was wondering what criteria is being used to filter the variants? I can't seem to find it in the documentation.

Thanks

KKJSP commented 1 year ago

@msteph11 The load functions documentation page has been updated with more details.

filter_variants:
If False, then all the variants are loaded. If True then only the filtered dna variants
are loaded. The filtered DNA variants are those that pass the Dna.filter_variants() function.
This list can be obtained by loading all variants by setting filter_variants=False and
then running Dna.filter_variants() on it. Information about the default filtered variants is
stored in the filtered column attribute of the Dna object.

Note: apply_filter in v2 has been renamed to filter_variants in v3 of mosaic. The above doc page is for v3.

KKJSP commented 1 year ago

Closing this for now. Feel free to comment if further clarification is required.