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, tree.use = NULL, genes.use = NULL,
thresh.use = 0.25, test.use = "bimod", ...)Seurat object
The node in the phylogenetic tree to use as a branch point
Can optionally pass the tree to be used. Default uses the tree in object@cluster.tree
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, 2013, 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), 'poisson', and 'negbinom'. The latter two options should only be used on UMI datasets, and assume an underlying poisson or negative-binomial distribution
Additional arguments passed to FindMarkers
Matrix containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)