Prepare SingleCellExperiment for use with iSEE

This function is intended to be used within the einprot workflows and assumes that the data has been processed as outlined in these.

prepareFinalSCE(sce, baseFileName, featureCollections, expType)

Arguments

sce

A SingleCellExperiment object.

baseFileName

Character scalar or NULL, the base file name of the output files. If NULL, no result files are generated.

featureCollections

List of CharacterLists with results from gene set testing.

expType

Character scalar, either "MaxQuant", "ProteomeDiscoverer", "FragPipe", "DIANN" or "Spectronaut".

Value

A SingleCellExperiment object. If baseFileName is not NULL, also save a text file with feature annotation columns that will not be included in the final SCE object.

Author

Charlotte Soneson