TrajAtlas.utils.getAttributeGEP#

TrajAtlas.utils.getAttributeGEP(adata, featureKey='pattern', sampleKey='sample', patternKey=None, cell_threshold=5, njobs=-1, bootstrap_iterations=0, **kwargs)[source]#

Get attribute (peak, expression, correlation) based on gene expression pattern axis with optional bootstrapping.

Parameters:

  • adata (AnnData) –

  • object. (Annotated data) –

  • featureKey (str) – The specific slot in adata.var that houses the gene-feature relationship information

  • sampleKey (str) – The specific slot in adata.obs that houses the sample information

  • patternKey (Optional[List]) – Pattern names. If not specific, we use all patterns in adata.obs.featureKey

  • cell_threshold (int) – Minimal cells to keep

  • njobs (int) – Number of cores to use

  • bootstrap_iterations (int) – Number of bootstrap iterations to perform. If 0, bootstrapping is not performed.

Returns:

MuData object. Contains correlation, expression, and peak modal.