runDiff: Calculate differential expression markers

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

Calculating differentially expressed markers

Usage

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

Arguments

object	a 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

A 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)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.