cometsc2: Marker genes discovery with COMETSC for autoencoder results

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

Marker genes discovery with COMETSC for autoencoder results

Description

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

Usage

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(s)

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

Examples

## Not run: 
    #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=",") 

## End(Not run)

kendomaniac/rCASC documentation built on June 10, 2025, 2:52 a.m.