Seurat (version 2.1.0)

DESeq2DETest: Differential expression using DESeq2

Description

Identifies differentially expressed genes between two groups of cells using DESeq2

Usage

DESeq2DETest(object, cells.1, cells.2, min.cells = 3, genes.use = NULL,
  assay.type = "RNA", ...)

Arguments

object

Seurat object

cells.1

Group 1 cells

cells.2

Group 2 cells

min.cells

Minimum number of cells expressing the gene in at least one of the two groups

genes.use

Genes to use for test

assay.type

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

...

Extra parameters to pass to DESeq2::results

Value

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

Details

This test does not support pre-filtering of genes based on average difference (or percent detection rate) between cell groups. However, genes may be pre-filtered based on their minimum detection rate (min.pct) across both cell groups. To use this method, please install DESeq2, using the instructions at https://bioconductor.org/packages/release/bioc/html/DESeq2.html

References

Love MI, Huber W and Anders S (2014). "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2." Genome Biology. https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Examples

# NOT RUN {
  pbmc_small
  DESeq2DETest(pbmc_small, cells.1 = WhichCells(object = pbmc_small, ident = 1),
              cells.2 = WhichCells(object = pbmc_small, ident = 2))
# }
# NOT RUN {
# }