find.markers.node

object

The node in the phylogenetic tree to use as a branch point

node

Genes to test. Default is to use all genes.

genes.use

Limit testing to genes which show, on average, at least
X-fold difference (log-scale) between the two groups of cells.<p></p><p>Increasing thresh.use speeds up the function, but can miss weaker signals.</p>

thresh.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)

test.use


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.


Seurat : R toolkit for single cell genomics

Satija Lab

Seurat

find.markers.node function

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.

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

Description

Usage

Arguments

Value