pegasus.search_de_genes

pegasus.search_de_genes(data, gene_list, rec_key='de_res', de_test='fisher', de_alpha=0.05, thre=1.5)[source]

Extract and display differential expression analysis results of markers for each cluster.

This function helps to see if markers are up or down regulated in each cluster via the interactive python environment:

  • ++ indicates up-regulated and fold change >= threshold;

  • + indicates up-regulated but fold change < threshold;

  • -- indicates down-regulated and fold change <= 1 / threshold;

  • - indicates down-regulated but fold change > 1 / threshold;

  • ? indicates not differentially expressed.

Parameters

  • data (MultimodalData or UnimodalData object) – Annotated data matrix containing the expression matrix and differential expression results.

  • gene_list (List[str]) – A list of gene symbols.

  • rec_key (str, optional, default: "de_res") – Keyword of DE analysis result stored in data.varm.

  • de_test (str, optional, default: "fisher") – Differential expression test to look at, could be either t, fisher or mwu.

  • de_alpha (float, optional, default: 0.05) – False discovery rate.

  • thre (float, optional, default: 1.5) – Fold change threshold to determine if the marker is a strong DE (++ or --) or weak DE (+ or -).

Returns

A data frame containing marker differential expression results for each cluster.

Return type

pandas.DataFrame

Examples

>>> df = pegasus.misc.search_de_genes(adata, ['CD3E', 'CD4', 'CD8'], thre = 2.0)