Seurat (version 2.3.4)

DESeq2DETest: Differential expression using DESeq2

Description

Identifies differentially expressed genes between two groups of cells using DESeq2

Usage

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

Arguments

object

Seurat object

cells.1

Group 1 cells

cells.2

Group 2 cells

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 {
# }