find.markers: Gene expression markers of identity classes

Description Usage Arguments Value

Description

Finds markers (differentially expressed genes) for identity classes

Usage

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find.markers(object, ident.1, ident.2 = NULL, genes.use = NULL,
  thresh.use = log(2), test.use = "bimod", min.pct = 0,
  print.bar = TRUE, only.pos = FALSE)

Arguments

object

Seurat object

ident.1

Identity class to define markers for

ident.2

A second identity class for comparison. If NULL (default) - use all other cells for comparison.

genes.use

Genes to test. Default is to use all genes.

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.

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)

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 expression

print.bar

Print a progress bar once expression testing begins (uses pbapply to do this)

only.pos

Only return positive markers (FALSE by default)

Value

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


paodan/studySeu documentation built on May 23, 2019, 3:06 p.m.