find.markers.node.Rd

% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/seurat.R
\name{find.markers.node}
\alias{find.markers.node}
\title{Gene expression markers of identity classes defined by a phylogenetic clade}
\usage{
find.markers.node(object, node, genes.use = NULL, thresh.use = log(2),
  test.use = "bimod")
}
\arguments{
\item{object}{Seurat object}

\item{node}{The node in the phylogenetic tree to use as a branch point}

\item{genes.use}{Genes to test. Default is to use all genes.}

\item{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.}

\item{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
identistics (p-values, ROC score, etc.)
}
\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.
}