runDiff {CytoTree} | R Documentation

## Calculate differential expression markers

### Description

Calculating differentially expressed markers

### Usage

    runDiff(object, branch.id = NULL, branch.id.2 = NULL, verbose = FALSE)

### Arguments

`object` | an CYT object
`branch.id` | vector. Branch ids use to run differentially expressed markers
`branch.id.2` | vector. Branch ids use to run differentially expressed markers in compare with branch.id
`verbose` | logic. Whether to print calculation progress.

### Value

An CYT object with cluster.id in meta.data

a data.frame with differential expressed markers

### See Also

`bulidTree`

### Examples

    cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
    cyt <- readRDS(file = cyt.file)

    DEG.table <- runDiff(cyt)

[Package CytoTree version 1.4.0 Index]