pegasus.de_analysis¶
-
pegasus.
de_analysis
(data, cluster, condition=None, subset=None, result_key='de_res', n_jobs=- 1, auc=True, t=True, fisher=False, mwu=False, temp_folder=None, verbose=True)[source]¶ Perform Differential Expression (DE) Analysis on data.
- Parameters
data (
anndata.AnnData
) – Annotated data matrix with rows for cells and columns for genes.cluster (
str
) – Cluster labels used in DE analysis. Must exist indata.obs
.condition (
str
, optional, default:None
) – Sample attribute used as condition in DE analysis. IfNone
, no condition is considered; otherwise, must exist indata.obs
.subset (
str
, optional, default:None
) – Perform DE analysis on only a subset of cluster IDs. Cluster ID subset is specified as"clust_id1,clust_id2,...,clust_idn"
, where all IDs must exist indata.obs[cluster]
.result_key (
str
, optional, default:"de_res"
) – Key name of DE analysis result stored.n_jobs (
int
, optional, default:-1
) – Number of threads to use. If-1
, use all available threads.auc (
bool
, optional, default:True
) – IfTrue
, calculate area under ROC (AUROC) and area under Precision-Recall (AUPR).t (
bool
, optional, default:True
) – IfTrue
, calculate Welch’s t test.fisher (
bool
, optional, default:False
) – IfTrue
, calculate Fisher’s exact test.mwu (
bool
, optional, default:False
) – IfTrue
, calculate Mann-Whitney U test.temp_folder (
str
, optional, default:None
) – Joblib temporary folder for memmapping numpy arrays.verbose (
bool
, optional, default:True
) – IfTrue
, show detailed intermediate output.
- Return type
None
- Returns
None
Update
data.varm
–data.varm[result_key]
: DE analysis result.
Examples
>>> pg.de_analysis(adata, cluster = 'spectral_leiden_labels')
subset: a comma-separated list of cluster labels. Then de will be performed only on these subsets.