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)
Value
Matrix containing a ranked list of putative markers, and associated
identistics (p-values, ROC score, etc.)