FindAllMarkers.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/differential_expression.R
\name{FindAllMarkers}
\alias{FindAllMarkers}
\alias{FindAllMarkersNode}
\title{Gene expression markers for all identity classes}
\usage{
FindAllMarkers(
  object,
  assay = NULL,
  features = NULL,
  logfc.threshold = 0.25,
  test.use = "wilcox",
  slot = "data",
  min.pct = 0.1,
  min.diff.pct = -Inf,
  node = NULL,
  verbose = TRUE,
  only.pos = FALSE,
  max.cells.per.ident = Inf,
  random.seed = 1,
  latent.vars = NULL,
  min.cells.feature = 3,
  min.cells.group = 3,
  pseudocount.use = 1,
  return.thresh = 0.01,
  ...
)
}
\arguments{
\item{object}{An object}

\item{assay}{Assay to use in differential expression testing}

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

\item{logfc.threshold}{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 logfc.threshold speeds up the function, but can miss weaker signals.}

\item{test.use}{Denotes which test to use. Available options are:
\itemize{
 \item{"wilcox"} : Identifies differentially expressed genes between two
 groups of cells using a Wilcoxon Rank Sum test (default)
 \item{"bimod"} : Likelihood-ratio test for single cell gene expression,
 (McDavid et al., Bioinformatics, 2013)
 \item{"roc"} : Identifies 'markers' of gene expression using ROC analysis.
 For each gene, evaluates (using AUC) a classifier built on that gene alone,
 to classify between two groups of cells. An AUC value of 1 means that
 expression values for this gene alone can perfectly classify the two
 groupings (i.e. Each of the cells in cells.1 exhibit a higher level than
 each of the cells in cells.2). An AUC value of 0 also means there is perfect
 classification, but in the other direction. A value of 0.5 implies that
 the gene has no predictive power to classify the two groups. Returns a
 'predictive power' (abs(AUC-0.5) * 2) ranked matrix of putative differentially
 expressed genes.
 \item{"t"} : Identify differentially expressed genes between two groups of
 cells using the Student's t-test.
 \item{"negbinom"} : Identifies differentially expressed genes between two
  groups of cells using a negative binomial generalized linear model.
  Use only for UMI-based datasets
 \item{"poisson"} : Identifies differentially expressed genes between two
  groups of cells using a poisson generalized linear model.
  Use only for UMI-based datasets
 \item{"LR"} : Uses a logistic regression framework to determine differentially
 expressed genes. Constructs a logistic regression model predicting group
 membership based on each feature individually and compares this to a null
 model with a likelihood ratio test.
 \item{"MAST"} : Identifies differentially expressed genes between two groups
 of cells using a hurdle model tailored to scRNA-seq data. Utilizes the MAST
 package to run the DE testing.
 \item{"DESeq2"} : Identifies differentially expressed genes between two groups
 of cells based on a model using DESeq2 which uses a negative binomial
 distribution (Love et al, Genome Biology, 2014).This test does not support
 pre-filtering of genes based on average difference (or percent detection rate)
 between cell groups. However, genes may be pre-filtered based on their
 minimum detection rate (min.pct) across both cell groups. To use this method,
 please install DESeq2, using the instructions at
 https://bioconductor.org/packages/release/bioc/html/DESeq2.html
}}

\item{slot}{Slot to pull data from; note that if \code{test.use} is "negbinom", "poisson", or "DESeq2",
\code{slot} will be set to "counts"}

\item{min.pct}{only test genes that are detected in a minimum fraction of
min.pct cells in either of the two populations. Meant to speed up the function
by not testing genes that are very infrequently expressed. Default is 0.1}

\item{min.diff.pct}{only test genes that show a minimum difference in the
fraction of detection between the two groups. Set to -Inf by default}

\item{node}{A node to find markers for and all its children; requires
\code{\link{BuildClusterTree}} to have been run previously; replaces \code{FindAllMarkersNode}}

\item{verbose}{Print a progress bar once expression testing begins}

\item{only.pos}{Only return positive markers (FALSE by default)}

\item{max.cells.per.ident}{Down sample each identity class to a max number.
Default is no downsampling. Not activated by default (set to Inf)}

\item{random.seed}{Random seed for downsampling}

\item{latent.vars}{Variables to test, used only when \code{test.use} is one of
'LR', 'negbinom', 'poisson', or 'MAST'}

\item{min.cells.feature}{Minimum number of cells expressing the feature in at least one
of the two groups, currently only used for poisson and negative binomial tests}

\item{min.cells.group}{Minimum number of cells in one of the groups}

\item{pseudocount.use}{Pseudocount to add to averaged expression values when
calculating logFC. 1 by default.}

\item{return.thresh}{Only return markers that have a p-value < return.thresh, or a power > return.thresh (if the test is ROC)}

\item{...}{Arguments passed to other methods and to specific DE methods}
}
\value{
Matrix containing a ranked list of putative markers, and associated
statistics (p-values, ROC score, etc.)
}
\description{
Finds markers (differentially expressed genes) for each of the identity classes in a dataset
}
\examples{
# Find markers for all clusters
all.markers <- FindAllMarkers(object = pbmc_small)
head(x = all.markers)
\dontrun{
# Pass a value to node as a replacement for FindAllMarkersNode
pbmc_small <- BuildClusterTree(object = pbmc_small)
all.markers <- FindAllMarkers(object = pbmc_small, node = 4)
head(x = all.markers)
}

}