Seurat (version 2.1.0)

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,
  assay.type = "RNA")

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

assay.type

Type of assay to fetch data for (default is RNA)

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))

# }