normalize_count: Normalize count data

In hjunwoo/ccfindR: Cancer Clone Finder

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))

hjunwoo/ccfindR documentation built on Oct. 4, 2019, 10:31 a.m.