integrationPblkae

This function execute integrationPblkae analysis which search for correspondence between clusters of two different experiments using clusters-pseudobulks generated using sparsely connected autoencoders. Thus, the function autoencoder4pseudoBulk has to be run in the two datasets before their comparison.

integrationPblkae(
  group = c("sudo", "docker"),
  scratch.folder,
  fileX = NULL,
  fileY = NULL,
  outputFolder,
  type = c("inter", "intra"),
  stats = c("anovalike", "pairwise")
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

scratch.folder,

a character string indicating the path of the scratch folder

fileX,

a character string indicating the path to the total.csv.for the 1st dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included.

fileY,

a character string indicating the path to the total.csv.for the 2nd dataset to be integrated. Total.csv is generated with autoencoder4pseudoBulk. File, with file name and extension included.

outputFolder,

where results are placed

type,

two values inter, intra. Inter refers to comparison among clusters of two independent experiments. Intra comparisons among clusters of the same experiment

stats,

two values anovalike, pairwise. Anovalike refers to comparison among clusters with respect to a pseudo reference sample. pairwise comparisons among all clusters by pairwise comparison

Value

a folder called psblkAE, which contains file called final_score.csv and all the intermediate files used to produce the integrated results.

Author

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

Examples

if (FALSE) {
 #inter
 library(rCASC)
 integrationPblkae(group="docker", 
        scratch.folder="/scratch", 
        fileX="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/setA1/permutation/total.csv",
        fileY="/data/clusters_association_paper/setA1_set1/set1/VandE/Results/set1/permutation/total.csv",
        outputFolder="/data/clusters_association_paper/setA1_set1",
        type="inter",
        stats="anovalike"
 )
 
 #intra
 library(rCASC)
 integrationPblkae(group="docker", 
        scratch.folder="/scratch", 
        fileX="/data/clusters_association_paper/setA1_set1/setA1/VandE/Results/setA1/permutation/total.csv",
        outputFolder="/data/clusters_association_paper/setA1_set1/setA1",
        type="intra",
        stats="pairwise"
 )
}