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.
FindMarkersNode(object, node, genes.use = NULL, thresh.use = log(2),
test.use = "bimod", ...)Seurat object
The node in the phylogenetic tree to use as a branch point
Genes to test. Default is to use all genes.
Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing thresh.use speeds up the function, but can miss weaker signals.
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)
Additional arguments passed to FindMarkers
Matrix containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)