FindMarkers: Gene expression markers of identity classes
In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description Usage Arguments Details Value References Examples

Finds markers (differentially expressed genes) for identity classes

FindMarkers(object, ...)

## Default S3 method:
FindMarkers(object, cells.1 = NULL, cells.2 = NULL,
  features = NULL, logfc.threshold = 0.25, test.use = "wilcox",
  min.pct = 0.1, min.diff.pct = -Inf, 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, ...)

## S3 method for class 'Seurat'
FindMarkers(object, ident.1 = NULL, ident.2 = NULL,
  assay = NULL, features = NULL, logfc.threshold = 0.25,
  test.use = "wilcox", min.pct = 0.1, min.diff.pct = -Inf,
  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, ...)

`object`	An object
`...`	Arguments passed to other methods and to specific DE methods
`cells.1`	Vector of cell names belonging to group 1
`cells.2`	Vector of cell names belonging to group 2
`features`	Genes to test. Default is to use all genes
`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.
`test.use`	Denotes which test to use. Available options are: "wilcox" : Identifies differentially expressed genes between two groups of cells using a Wilcoxon Rank Sum test (default) "bimod" : Likelihood-ratio test for single cell gene expression, (McDavid et al., Bioinformatics, 2013) "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)) ranked matrix of putative differentially expressed genes. "t" : Identify differentially expressed genes between two groups of cells using the Student's t-test. "negbinom" : Identifies differentially expressed genes between two groups of cells using a negative binomial generalized linear model. Use only for UMI-based datasets "poisson" : Identifies differentially expressed genes between two groups of cells using a poisson generalized linear model. Use only for UMI-based datasets "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. "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. "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
`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
`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
`verbose`	Print a progress bar once expression testing begins
`only.pos`	Only return positive markers (FALSE by default)
`max.cells.per.ident`	Down sample each identity class to a max number. Default is no downsampling. Not activated by default (set to Inf)
`random.seed`	Random seed for downsampling
`latent.vars`	Variables to test, used only when `test.use` is one of 'LR', 'negbinom', 'poisson', or 'MAST'
`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
`min.cells.group`	Minimum number of cells in one of the groups
`pseudocount.use`	Pseudocount to add to averaged expression values when calculating logFC. 1 by default.
`ident.1`	Identity class to define markers for; pass an object of class `phylo` or 'clustertree' to find markers for a node in a cluster tree; passing 'clustertree' requires `BuildClusterTree` to have been run
`ident.2`	A second identity class for comparison; if `NULL`, use all other cells for comparison; if an object of class `phylo` or 'clustertree' is passed to `ident.1`, must pass a node to find markers for
`assay`	Assay to use in differential expression testing

p-value adjustment is performed using bonferroni correction based on the total number of genes in the dataset. Other correction methods are not recommended, as Seurat pre-filters genes using the arguments above, reducing the number of tests performed. Lastly, as Aaron Lun has pointed out, p-values should be interpreted cautiously, as the genes used for clustering are the same genes tested for differential expression.

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

McDavid A, Finak G, Chattopadyay PK, et al. Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics. 2013;29(4):461-467. doi:10.1093/bioinformatics/bts714

Trapnell C, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology volume 32, pages 381–386 (2014)

Andrew McDavid, Greg Finak and Masanao Yajima (2017). MAST: Model-based Analysis of Single Cell Transcriptomics. R package version 1.2.1. https://github.com/RGLab/MAST/

Love MI, Huber W and Anders S (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome Biology. https://bioconductor.org/packages/release/bioc/html/DESeq2.html

# Find markers for cluster 2
markers <- FindMarkers(object = pbmc_small, ident.1 = 2)
head(x = markers)

# Pass 'clustertree' or an object of class phylo to ident.1 and
# a node to ident.2 as a replacement for FindMarkersNode
pbmc_small <- BuildClusterTree(object = pbmc_small)
markers <- FindMarkers(object = pbmc_small, ident.1 = 'clustertree', ident.2 = 5)
head(x = markers)