A function to select DE genes
selectDEgenes( sce = NULL, de_res = NULL, altExp_name = "none", pval_adj = 0.05, mean_diff = 0, pct_diff = 0.1, topN = 10 )
| sce | A SingleCellExperiment object with DE results stored in meta data DE_res list. |
|---|---|
| de_res | DE_res returned by DEgenesCross(). |
| altExp_name | A character indicates which expression matrix is used. by default is none (i.e. RNA). |
| pval_adj | A numeric indicates the threshold of adjusted p-value. |
| mean_diff | A numeric indicates the threshold of difference of average expression. |
| pct_diff | A numeric indicates the threshold of difference of percentage expression. |
| topN | A numeric indicates the top number of genes will be included in the list. |
A SingleCellExperiment With filtered DE results in DE_res_filter list of metadata
data(sce_control_subset) sce_control_subset <- DEgenes(sce_control_subset, group = sce_control_subset$SNF_W_louvain, return_all = TRUE, exprs_pct = 0.5) sce_control_subset <- selectDEgenes(sce_control_subset)