Database weight matrix - Githubissues

bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data

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Database weight matrix #4

Open Jayjay601 opened 4 years ago

Jayjay601 commented 4 years ago

Hi! I'm just wondering what is database weight matrix, W? If users don't provide their own markers db, W will be 1? And if they do provide their own markers, what is W?

Thanks! J

bioinfo-ibms-pumc commented 4 years ago

Hi, Jayjay601. In this version, If both user own marker db and cellmarker db were used, the database weights were fixed to 0.9 and 0.1, respectively. This is because we believe user's definition is far more important than the cellmarker db. If you want a custom weight, just modified the variable wm in get_cell_matrix function. No parameter was provided in the command line now. Sorry for inconvenience.