A function to perform DE analysis on CITE seq data
DEgenes( sce, altExp_name = "none", exprs_value = "logcounts", group = NULL, method = "wilcox", exprs_pct = 0.1, exprs_threshold = 0, return_all = FALSE, pval_adj = 0.05, mean_diff = 0, pct_diff = 0.1, topN = 10 )
| sce | A SingleCellExperiment object |
|---|---|
| altExp_name | A character indicates which expression matrix is used. by default is none (i.e. RNA). |
| exprs_value | A character indicates which expression value in assayNames is used. |
| group | A vector indicates the grouping of the data |
| method | A character indicates the method used in DE analysis |
| exprs_pct | A numeric indicates the threshold expression percentage of a gene to be considered in DE analysis |
| exprs_threshold | A numeric indicates the threshold of expression. By default is 0. |
| return_all | Whether return full list of DE genes |
| 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 SingleCellExeperiment with DE results stored in meta data DE_res
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)