normalize_count {ccfindR} | R Documentation

## Normalize count data

### Description

Rescale count matrix entries such that all cells have the same library size.

### Usage

    normalize_count(object)

### Arguments

`object` | `scNMFSet` object.

### Details

For analysis purposes, it is sometimes useful to rescale integer count data into floats such that all cells have the same median counts. This function will calculate the median of all UMI counts of cells (total number of RNAs derived from each cell). All count data are then rescaled such that cells have uniform UMI count equal to the median.

### Value

`scNMFSet` object with normalized count data.

### Examples

    library(Matrix)
    set.seed(1)
    s <- scNMFSet(count=matrix(rpois(n=1200,lambda=3),40,30))
    colMeans(counts(s))
    s <- normalize_count(s)
    colMeans(counts(s))

[Package ccfindR version 1.4.2 Index]