scSemiProfiler_dev.singlecell_process.scprocess¶
-
scSemiProfiler_dev.singlecell_process.scprocess(name, singlecell, normed='yes', cellfilter='no', threshold=0.001, geneset='human', weight=0.5, k=15)[source]¶ Process the reprsentatives’ single-cell data, including preprocessing and feature augmentations.
- Parameters
name (
str) – Project name.singlecell (
str) – Path to representatives’ single-cell data.normed (
str) – Whether the data has been library size normed or not.cellfilter (
str) – Whether to perform cell selection.threshold (
float) – Threshold for background noise removal.geneset (
str) – Gene set file name.weight (
float) – The proportion of top features to increase importance weight.k (
int) – K for the K-NN graph built for cells.
Example
>>> scSemiProfiler.scprocess(name='project_name',singlecell=name+'/representative_sc.h5ad',normed='yes',cellfilter='no',threshold=1e-3,geneset='yes',weight='yes',k=15)
- Return type