size_factor: Size factor of each cell

In jichunxie/CDI: Clustering Deviation Index (CDI)

Size factor of each cell

Description

Different cells have different library sizes. This function calculates the size factor of each cell in the UMI count matrix to capture the variation in cell library size.

Usage

size_factor(X, count_slot = NULL)

Arguments

X	The class of X can be "matrix", "Seurat" object, or "SingleCellExperiment" object. If X is a matrix, it should be a raw UMI count matrix where each row represents a gene, and each column represents a cell. The genes should be those before feature gene selection. If X is a Seurat object or SingleCellExperiment object, users need to specify where the count matrix is stored in count_slot.
count_slot	A string indicating the location of raw UMI count. For Seurat object, it is a slot in "RNA" of "assays"; For SingleCellExperiment object, it is a slot in "assays". Each row represents a gene, and each column represents a cell. The genes should be those before feature gene selection.

Value

A numeric vector indicating the size factor of the cells. This should be one of the inputs of the function calculate_CDI.

Examples

ng <- 100; nc <- 100
set.seed(1)
X <- cbind(
	matrix(
		c(rnbinom(ng*nc/4, size = 1, mu = 0.1),
			rnbinom(ng*nc/4, size = 1, mu = 0.5)),
		nrow = ng, 
		byrow = TRUE),
	matrix(
		c(rnbinom(ng*nc/4, size = 1, mu = 1),
			rnbinom(ng*nc/4, size = 1, mu = 0.5)),
		nrow = ng, 
		byrow = TRUE))
colnames(X) <- paste0('c', seq_len(nc))
rownames(X) <- paste0('g', seq_len(ng))

## Input: matrix
cell_size <- size_factor(X = X)

## Input: SingleCellExperiment object
library(SingleCellExperiment)
sim_sce <- SingleCellExperiment(
  list(count = X),
  colData = data.frame(Cell_name = colnames(X)),
	 rowData = data.frame(Gene_name = rownames(X)))
cell_size <- size_factor(X = sim_sce, count_slot = "count")

## Input: Seurat object
library(Seurat)
library(SeuratObject)
sim_seurat <- CreateSeuratObject(counts = as.data.frame(X))
sim_seurat <- AddMetaData(sim_seurat, colnames(X), "Cell_name")
cell_size <- size_factor(X = sim_seurat, count_slot = "counts")

jichunxie/CDI documentation built on Dec. 6, 2023, 5:48 a.m.