preprocessing: preprocessing

In scTEP: Single-Cell Trajectory Inference using Ensemble Pseudotimes

preprocessing

Description

Conduct preprocessing, including remove all zero columns and scale gene expression smaller than 100 by log transformation with 2 as base.

Usage

preprocessing(expr)

Arguments

expr	The gene expression matrix.

Value

List with the following keys:

• expr - Gene expression matrix, with rows represent samples and columns represent genes.

Examples

#Load the package
library(scTEP)
#Load example data
data("goolam")
#Get data matrix
expr <- as.matrix(t(SummarizedExperiment::assay(goolam)))

data = preprocessing(expr)

scTEP documentation built on Sept. 26, 2022, 5:10 p.m.