defRootCells {CytoTree} | R Documentation

## definition of root cells

### 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)

[Package CytoTree version 1.0.3 Index]