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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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some questions about the function score_eRegulons #369

Closed aaaaaaaaaayong closed 1 month ago

aaaaaaaaaayong commented 2 months ago

I successfully finished running the upstream process of the lasted version of the SCENICplus.But when I was doing downstream analysis, I ran into a problem.

I want score eRegulon target genes and regions in cells using AUC algorithm by using score_eRegulons.This is the help description for this function:

score_eRegulons( eRegulons: pd.DataFrame, gex_mtx: pd.DataFrame, acc_mtx: pd.DataFrame, auc_threshold: float = 0.05, normalize: bool = False, n_cpu: int = 1 )

I don't understand what gex_mtx, acc_mtx refers to pd.DataFrame.

SeppeDeWinter commented 2 months ago

Hi @aaaaaaaaaayong

This is how you should use the function:


import mudata

mdata = mudata.read(<PATH_TO_MUDATA_OUTPUT>)

gene_region_AUC = score_eRegulons(
        eRegulons=mdata.uns["direct_e_regulon_metadata"],
        gex_mtx=mdata["scRNA"].to_df(),
        acc_mtx=mdata["scATAC"].to_df(),
        n_cpu=1)

I hope that helps?

All the best,

Seppe

aaaaaaaaaayong commented 1 month ago

Hi@SeppeDeWinter

Thanks for your help, this actually worked successfully.

Thank you and wish you all the best.

ayong