Seurat (version 2.1.0)

NegBinomRegDETest: Negative binomial test for UMI-count based data (regularized version)

Description

Identifies differentially expressed genes between two groups of cells using a likelihood ratio test of negative binomial generalized linear models where the overdispersion parameter theta is determined by pooling information across genes.

Usage

NegBinomRegDETest(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 data frame of test results.

Examples

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

# }