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Irrationone / cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data
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Basic usability enhancements #37

Open kieranrcampbell opened 5 years ago

kieranrcampbell commented 5 years ago

For paper acceptance / bioconductor submission, we should aim to have the following usability enhancements:

  1. Allow multiple ways of passing the marker matrix - ie let the user pass the named list and have cellassign call marker_list_to_mat with nice errors if something fails
  2. If the SCE doesn't match the number of marker genes, can we try to do something intelligent with subsetting? Ie work out if the rownames look like ensmebl IDs or symbols, and try and subset the sce based on rowData(sce)$Symbol or rowData(sce)$ID ?
  3. If SCE already has size factors, use them if s isn't provided (and should we change s to size_factors anyway? bad name)

^^ all of the above should throw a message to the user warning them of what the software is up to and that results aren't guaranteed