find.markers.node: Gene expression markers of identity classes defined by a...

Description Usage Arguments Value

Description

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.

Usage

1
2
find.markers.node(object, node, genes.use = NULL, thresh.use = log(2),
  test.use = "bimod", ...)

Arguments

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)

Value

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


paodan/studySeu documentation built on May 23, 2019, 3:06 p.m.