Description Usage Arguments Value
Finds markers (differentially expressed genes) for identity classes
1 2 3 |
object |
Seurat object |
ident.1 |
Identity class to define markers for |
ident.2 |
A second identity class for comparison. If NULL (default) - use all other cells for comparison. |
genes.use |
Genes to test. Default is to use all genes. |
thresh.use |
Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Increasing thresh.use speeds up the function, but can miss weaker signals. |
test.use |
Denotes which test to use. Seurat currently implements "bimod" (likelihood-ratio test for single cell gene expression, McDavid et al., Bioinformatics, 2011, default), "roc" (standard AUC classifier), "t" (Students t-test), and "tobit" (Tobit-test for differential gene expression, as in Trapnell et al., Nature Biotech, 2014) |
min.pct |
- only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expression |
print.bar |
Print a progress bar once expression testing begins (uses pbapply to do this) |
only.pos |
Only return positive markers (FALSE by default) |
Matrix containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.