dePblkae: dePblkae

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

dePblkae

Description

This function execute dePblkae analysis which detects differentiale expressed genes among clusters using a pseudobulk generated with autoencoders: autoencoder4pseudoBulk function. It is advisible to do the analysis on a dataset made of at least 20 permutation

Usage

dePblkae(group = c("sudo", "docker"), data.folder, scratch.folder)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
data.folder	folder where the total.csv file is located
scratch.folder	where calculation is performed

Value

a file called DE.txt, which contains for each cluster the ID of the genes detected as DE, a file called log2_reformatedCPM.psblkAE.csv, which contains the log2 CPM of the psblkAE file and a file log2_reformatedCPM.psblkAE_mean-centered.csv, where log2 CPM are mena centered.

Author(s)

Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino

Examples

## Not run: 
 library(rCASC)
 dePblkae(group="docker", 
        data.folder="/somewhere/in/your/PC", 
        scratch.folder="/scratch"
 )

## End(Not run)

kendomaniac/rCASC documentation built on July 3, 2024, 6:05 a.m.