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ENH: Adding new action to normalize FeatureTable[Frequency] #311

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VinzentRisch opened this issue Jul 19, 2024 · 0 comments
Open

ENH: Adding new action to normalize FeatureTable[Frequency] #311

VinzentRisch opened this issue Jul 19, 2024 · 0 comments
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@VinzentRisch
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VinzentRisch commented Jul 19, 2024

Addition Description
When creating a FeatureTable[Frequency] by mapping reads to reference genes, the resulting data is total amount of reads that mapped to a gene. With this data it is impossible to make comparisons inside a sample, because of different gene lengths and it is also impossible to make comparisons between samples because of different total amount of reads per sample. To solve this issue I propose a new action that can normalize the tables with various methods. The python package used for this action will be RNAnorm.

The action will take as inputs FeatureTable[Frequency] and SequenceCharacteristics[Length]. And it will output FeatureTable[Normalized], that will be added to q2-types with qiime2/q2-types#339.
There will be properties added to the output indicating the method used.

See here for details on the different methods.

References
https://forum.qiime2.org/t/2024-07-03-group-meeting/30649/5

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