Marker genes discovery with COMETSC for autoencoder results

This function executes a ubuntu docker for cometsc (https://github.com/MSingerLab/COMETSC)

cometsc2(
  group = c("sudo", "docker"),
  file,
  scratch.folder,
  threads = 1,
  X = 0.15,
  K = 2,
  counts = c("True", "False"),
  skipvis = c("True", "False"),
  nCluster,
  separator,
  clustering.output
)

Arguments

group,

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

file,

a character string indicating the path of the file, with file name and extension included

scratch.folder,

temporary folder where calculation is made

threads,

integer refering to the max number of process run in parallel default 1 max the number of clusters under analysis, i.e. nCluster

X,

from 0 to 1 argument for XL-mHG default 0.15, for more info see cometsc help.

K,

the number of gene combinations to be considered., possible values 2, 3, 4, default 2. WARNING increasing the number of combinations makes the matrices very big

counts,

if set to True it will graph the log(expression+1). To be used if unlogged data are provided

skipvis,

set to True to skip visualizations

nCluster,

number of interested cluster used for analysis

separator,

separator used in count file, e.g. '\t', ','

clustering.output,

path of the clustering.output file to use

Value

folders with prefix output. More info in output at https://hgmd.readthedocs.io/en/latest/Output.html

Author

Raffaele Calogero,raffaele.calogero [at] unito [dot] it, University of Torino

Examples

if (FALSE) {
    #running cometsc
    cometsc(group="docker", file="/Users/raffaelecalogero/Desktop/AXLN1/data/topx_veanno.csv", 
           scratch.folder="/Users/raffaelecalogero/Desktop",
           threads=1, counts="True", skipvis="False", nCluster=8, separator=",") 
}