pegasus.pseudo.markers
- pegasus.pseudo.markers(pseudobulk, head=None, de_key='deseq2', alpha=0.05)[source]
Extract pseudobulk DE results into a human readable structure.
This function extracts information from
data.varm[de_key]
, and return as a human readible dictionary of pandas DataFrame objects.- Parameters
pseudobulk (
UnimodalData
) – Pseudobulk data matrix with rows for cells and columns for genes.head (
int
, optional, default:None
) – List only tophead
genes. IfNone
, show any DE genes.de_key (
str
, optional, default,deseq2
) – Keyword of DE result stored indata.varm
.alpha (
float
, optional, default:0.05
) – q-value threshold for getting significant DE genes. Only those with q-value of MWU test no less thanalpha
are significant, and thus considered as DE genes.
- Returns
results – A Python dictionary containing DE results. This dictionary contains two keywords: ‘up’ and ‘down’. ‘up’ refers to up-regulated genes, which should have ‘log2FoldChange’ > 0.5. ‘down’ refers to down-regulated genes, which should have ‘log2FoldChange’ < 0.5.
- Return type
Dict[str, pd.DataFrame]
Examples
>>> markers = pg.pseudo.markers(pseudobulk)