defRootCells: definition of root cells

In CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

definition of root cells

Usage

defRootCells(object, root.cells = NULL, verbose = FALSE)

Arguments

object	a CYT object
root.cells	vector. Cell name of the root cells
verbose	logical. Whether to print calculation progress.

Value

A CYT object

Examples

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

# Define root cells by cluster
cyt <- defRootCells(cyt, root.cells = 6, verbose = TRUE)
cyt <- defRootCells(cyt, root.cells = c(6,8), verbose = TRUE)

# Define root cells by cell names
meta.data <- fetchPlotMeta(cyt)
cells <- meta.data$cell[which(meta.data$stage == "D0")]
cells <- as.character(cells)
cyt <- defRootCells(cyt, root.cells = cells, verbose = TRUE)

CytoTree documentation built on Nov. 10, 2020, 2 a.m.