Seurat (version 2.0.1)

NegBinomDETest: Negative binomial test for UMI-count based data

Description

Identifies differentially expressed genes between two groups of cells using a negative binomial generalized linear model

Usage

NegBinomDETest(object, cells.1, cells.2, genes.use = NULL,
  latent.vars = NULL, print.bar = TRUE, min.cells = 3)

Arguments

object

Seurat object

cells.1

Group 1 cells

cells.2

Group 2 cells

genes.use

Genes to use for test

latent.vars

Latent variables to test

print.bar

Print progress bar

min.cells

Minimum number of cells threshold

Value

Returns a p-value ranked matrix of putative differentially expressed genes.

Examples

# NOT RUN {
pbmc_small
# Note, not recommended for particularly small datasets - expect warnings
NegBinomDETest(pbmc_small, cells.1 = WhichCells(object = pbmc_small, ident = 1),
            cells.2 = WhichCells(object = pbmc_small, ident = 2))

# }