cell.gating: Run PCA on the main data

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Run PCA on the main data

Description

This function takes an object of class scSeqR and runs PCA on the main data.

Usage

cell.gating(x = NULL, my.plot = NULL)

Arguments

x	An object of class scSeqR.
clust.method	Choose from "base.mean.rank" or "gene.model", defult is "base.mean.rank".
top.rank	A number taking the top genes ranked by base mean, defult = 500.
gene.list	A list of genes to be used for PCA. If "clust.method" is set to "gene.model", defult = "my_model_genes.txt".

Value

An object of class scSeqR.

Examples

## Not run: 
my.obj <- run.pca(my.obj, clust.method = "gene.model", gene.list = "my_model_genes.txt")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.