API

sigc_score

Get a set of signature score of a given gene expression matrix.

param ex_mtx

The expression profile matrix. The rows should correspond to different cells, the columns to different genes (n_cells x n_genes).

param GeneSigs

A dataframe with columns [“name”, “member”, “description”]. name member description signature1 gene1 signature1 description signature1 gene2 signature1 description signature2 gene4 signature2 description

param method

sinature score method [AUCell, GSVA, ssGSEA, …] (default: AUCell).

param threshold

if method param select AUCell then threshold means: The fraction of the ranked genome to take into account for the calculation of the Area Under the recovery Curve.

param num_workers

The number of cores to use in AUCell method (default: 4).

return

A dataframe with cell signature score (n_cells x n_signatures).

genesets2GeneSig

Conver dataframe to GeneSig for AUCell.

param df

A dataframe with columns [“name”, “member”, “description”]. name member description signature1 gene1 signature1 description signature1 gene2 signature1 description signature2 gene4 signature2 description

return

GeneSignature list.