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
orUnimodalData
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 indata.varm
.de_test (
str
, optional, default:"fisher"
) – Differential expression test to look at, could be eithert
,fisher
ormwu
.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)