normalizeTomo: Normalize data

In tomoda: Tomo-seq data analysis

Description

Normalize the raw read count in a SummarizedExperiment object.

Usage

normalizeTomo(object, method = "median")

Arguments

object	A SummarizedExperiment object.
method	Character, must be one of "median", or "cpm".

Details

This function should be run for SummarizedExperiment object created from raw read count matrix. If the SummarizedExperiment object already has a normalized count matrix. The function simply return the original object. Library sizes of all sections are normalized to the median library size (method='median') or one million (method='cpm').

Value

A SummarizedExperiment object with normalized read count matrix saved in assay 'normalized'.

Examples

data(zh.data)
zh <- createTomo(zh.data, normalize=FALSE)
zh <- normalizeTomo(zh)

tomoda documentation built on Nov. 8, 2020, 8:10 p.m.