uniport.TFIDF_LSI
- uniport.TFIDF_LSI(adata, n_comps=50, binarize=True, random_state=0)[source]
Computes LSI based on a TF-IDF transformation of the data from MultiMap. Putative dimensionality reduction for scATAC-seq data. Adds an
.obsm['X_lsi']field to the object it was ran on.Input
- adata
AnnData The object to run TFIDF + LSI on. Will use
.Xas the input data.- n_comps
int The number of components to generate. Default: 50
- binarize
bool Whether to binarize the data prior to the computation. Often done during scATAC-seq processing. Default: True
- random_state
int The seed to use for randon number generation. Default: 0
- adata