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[Code Refactor]: Add cetygo into cell type check QC report #127

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ejh243 opened this issue Apr 30, 2024 · 1 comment
Open

[Code Refactor]: Add cetygo into cell type check QC report #127

ejh243 opened this issue Apr 30, 2024 · 1 comment
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@ew367
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DNAm DNA methylation array enhancement New feature or request

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@ejh243
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ejh243 commented Apr 30, 2024

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[email protected]

Path to affected file

array/DNAm/preprocessing/QCwithinCellType.rmd

Type of refactor

Code optimisation

Description of required code refactor

Currently we do cetygo after cell type check and normalisation. Would it make sense to include the plots etc into the array/DNAm/preprocessing/QCwithinCellType.rmd. This would mean running array/DNAm/preprocessing/CETYGOdeconvolution.r after the array/DNAm/preprocessing/clusterCellTypes.r.

We might also want to add some default thresholds to the config file.
@ejh243 ejh243 added enhancement New feature or request DNAm DNA methylation array labels Apr 30, 2024
@ejh243
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ejh243 commented Apr 30, 2024

Also add cetygo output to QC metrics file?

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DNAm DNA methylation array enhancement New feature or request
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