Cnv.filter_amplicons

missionbio.mosaic.cnv.Cnv.filter_amplicons

Cnv.filter_amplicons(completeness: float = 50, read_depth: int = 10) → ndarray

Remove amplicons with missing information.

Parameters:

completenessfloat [0, 100]

The minimum percentage of barcodes for an amplicon that must have reads greater than or equal to read_depth to keep that amplicon.

read_depthint

The minimum required depth for each amplicon-barcode to not be considered as missing during the completness calculation.

Returns:

np.ndarray

The list of amplicons with completeness greater than the threshold.

Notes

The “completeness” parameter here has a different meaning from the completeness parameter in the context of [cell calling](https://support.missionbio.com/hc/en-us/articles/360042381634-Cell-calling)

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< Class Cnv