subsetCYT: subset CYT object

In CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

This subsets an CYT object by given a list of cells or cluster id. This function will subset all results without recalculating them, such as knn, PCA, tSNE, umap and pseudotime. For instance, you can choose recalculate PCA and tSNE and destiny scores by paramter recalculate.

Usage

subsetCYT(object, cells = NULL, knn = NA, verbose = FALSE)

Arguments

object	A CYT object
cells	vector, Names of the cells to retain.
knn	numeric. If is NA, the KNN will be equal to the knn number in the input CYT object.
verbose	logic. Whether to print calculation progress.

Value

A CYT object

Examples

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

meta.data <- fetchPlotMeta(cyt)
cells <- meta.data$cell[which(meta.data$stage == "D0")]
sub.cyt <- subsetCYT(cyt, cells = cells)
sub.cyt

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