Finds markers (differentially expressed genes) for each of the identity classes in a dataset
FindAllMarkers(object, genes.use = NULL, thresh.use = 0.25,
test.use = "bimod", min.pct = 0.1, min.diff.pct = 0.05,
print.bar = TRUE, only.pos = FALSE, max.cells.per.ident = Inf,
return.thresh = 0.01, do.print = FALSE, random.seed = 1,
min.cells = 3, latent.vars = "nUMI")Seurat object
Genes to test. Default is to all genes
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.
Denotes which test to use. Seurat currently implements "bimod" (likelihood-ratio test for single cell gene expression, McDavid et al., Bioinformatics, 2013, 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), 'poisson', and 'negbinom'. The latter two options should only be used on UMI datasets, and assume an underlying poisson or negative-binomial distribution
- 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 expression
- only test genes that show a minimum difference in the fraction of detection between the two groups. Set to -Inf by default
Print a progress bar once expression testing begins (uses pbapply to do this)
Only return positive markers (FALSE by default)
Down sample each identity class to a max number. Default is no downsampling.
Only return markers that have a p-value < return.thresh, or a power > return.thresh (if the test is ROC)
FALSE by default. If TRUE, outputs updates on progress.
Random seed for downsampling
Minimum number of cells expressing the gene in at least one of the two groups
remove the effects of these variables
Matrix containing a ranked list of putative markers, and associated statistics (p-values, ROC score, etc.)