File	Date	Author	Commit
ReadMe.txt	2018-05-07	Andrzej MIZERA	[162488] Initial commit
SynergisticCore.R	2018-05-07	Andrzej MIZERA	[162488] Initial commit

Read Me

Requirements
------------

- R (https://www.r-project.org/) version 3.4.0 or higher

- Additional R packages: parallel, infotheo
 
Data file format
----------------

SynergisticCore.R accepts data in the CSV format, where columns contain expression profiles
of individaul cells and rows consists of expressions of individual genes in cells.

The first column contains gene names and the first row contains the header with columns, i.e.
cells, identifiers. A cell identifier should be of the format
  
  subpopulation_identifier.cell_number

For example: 
  
  Neuron.1 (cell one in the Neuron subpopulation),
  Neuron.2 (cell two in the Neuron subpopulation),
  NSC.1 (cell one in the NSC subpopulation),
  NSC.2 (cell two in the NSC subpopulation),
  Astro.1 (cell one in the astrocytes subpopulation).

The subpopulation identifiers in column identifiers are used to determine the target subpopulation and optionally subpopulations excluded from background subpopulations
(see Usage section below).

Usage:
------

> Rscript SynergisticCore.R <datafile> <Expression threshold> <target subpopulation id>
  [-E <number of excluded subpopulations> <excluded subpopulation id 1> <excluded
   subpopulation id 2> ... ]

where

- datafile: a file in the format specified above containing single-cell RNA-seq data
  for a number of subpopulations,
- expression threshold: a number specifying the threshold value below which a gene is
  considered not to be expressed,
- target subpopulation id: identifier of the subpopulation for which the synergistic 
  identity core is searched. 

Optionally, certain subpopulations can be excluded from the set of background subpopulations. For that the -E option can be used followed by the number of subpopulations and the identifiers of the subpopulations to be excluded.

Usage examples:
---------------

> Rscript SynergisticCore.R "Data/data_LlorensBodadilla_for_totalCorrelation.csv" 1 a1_young

> Rscript SynergisticCore.R "Data/Test_data/data_Scialdone2016_for_totalCorrelation_new.csv" 10 Blood_progenitors -E 1 Unspecified

> Rscript SynergisticCore.R "Data/data_Grun_2015_for_totalCorrelation.csv" 1 Enterocyte -E 1 undefined