tomas.lrt.total_mRNA_aware_DE
- tomas.lrt.total_mRNA_aware_DE(adata_rc, groupby, reference=None, groups=None, minCells=5, n_cores=None, pval_cutoff=0.05, logFC_cutoff=0, method='wilcoxon')
Total-mRNA-aware differential expression analysis. :param adata_rc: The ratio-based corrected UMI counts.
Rows correspond to droplets and columns to genes.
- Parameters:
groupby (str) – The key of the droplet categories stored in adata.obs.
reference (str) – One droplet category annotated in adata.obs[groupby]. Compare with respect to the specified group.
groups (list, optional) – Droplet categories annotated in adata.obs[groupby] to which DE analysis shoudl be performed with. The default is None.
minCells (int, optional) – Minimum number of cells in one of the group. The default is 5.
n_cores (int, optional) – Number of cpu cores be used. If not given, generally 80% cpu cores woueld be used.
pval_cutoff (float, optional) – Significance level. The default is 0.05.
logFC_cutoff (float, optional) – Cutoff of log2-foldchange to tell the DE significance. The default is 0.
method (str, optional) – The method to perform DE analysis, such as ‘wilcoxon’ or ‘lrt’. The default is ‘wilcoxon’.
- Returns:
lrt_DE_dic – Return total-mRNA-aware DE results in a dictionary. The keys are homo-typic droplet categories compared to the reference.
- Return type: