Normalize: Normalize

In bicciatolab/PoPsicleR: Pipeline of Preprocessing for Single Cell Experiment

Normalize

Description

Perform data normalization on the provided input. User must define the number of variable genes to be investigated after normalization.

Usage

Normalize(UMI, variable_genes=2000, out_folder=getwd())

Arguments

UMI	Input UMI object generated via previous popsicleR functions
variable_genes	Number of highly variable genes investigated after normalization. Default is 2000
out_folder	Output folder. Default is the working directory

Details

Normalize returns two graphs in the "02.PreProcessing" folder:

the first graph (02a) shows expression before and after the normalization step,

while the second (02b) highlights the highly variable genes.

Value

Returns a Seurat Object after normalization process.

Author(s)

Jimmy Caroli, Francesco Grandi

Examples

Normalize(seurat_object, variable_genes=2000)

bicciatolab/PoPsicleR documentation built on May 7, 2024, 7:26 a.m.