Seurat (version 2.1.0)

DiffExpTest: Likelihood ratio test for zero-inflated data

Description

Identifies differentially expressed genes between two groups of cells using the LRT model proposed in McDavid et al, Bioinformatics, 2013

Usage

DiffExpTest(object, cells.1, cells.2, assay.type = "RNA", genes.use = NULL,
  print.bar = TRUE)

Arguments

object

Seurat object

cells.1

Group 1 cells

cells.2

Group 2 cells

assay.type

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

genes.use

Genes to test. Default is to use all genes

print.bar

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

Value

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

Examples

# NOT RUN {
pbmc_small
DiffExpTest(pbmc_small, cells.1 = WhichCells(object = pbmc_small, ident = 1),
            cells.2 = WhichCells(object = pbmc_small, ident = 2))

# }