Seurat (version 2.1.0)

TobitTest: Differential expression testing using Tobit models

Description

Identifies differentially expressed genes between two groups of cells using Tobit models, as proposed in Trapnell et al., Nature Biotechnology, 2014

Usage

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

Arguments

object

Seurat object

cells.1

Group 1 cells

cells.2

Group 2 cells

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)

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