dePblkae

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

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

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

Examples

if (FALSE) {
 library(rCASC)
 dePblkae(group="docker", 
        data.folder="/somewhere/in/your/PC", 
        scratch.folder="/scratch"
 )
}