Seurat (version 2.0.1)

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)

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 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)
)

# }