Description Usage Arguments Value
Finds markers (differentially expressed genes) based on a branching point (node) in the phylogenetic tree. Markers that define clusters in the left branch are positive markers. Markers that define the right branch are negative markers.
1 2 | find.markers.node(object, node, genes.use = NULL, thresh.use = log(2),
test.use = "bimod", ...)
|
object |
Seurat object |
node |
The node in the phylogenetic tree to use as a branch point |
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) |
Matrix containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)
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