NARROMI

Narromi is an MI based algorithm that tries to minimize noise in the MI using linear programming. It is published in [Zhang2013] .

Running Narromi

Narromi needs a minimum of two input files:

  • -i, --infile: An expression matrix (genes are columns, samples are rows) without headers.
  • -g, --genes: A file containing gene names that correspond to columns in the expression matrix.

Here is an example matrix containing expression data for five genes in ten samples:

0.4254475 0.0178292 0.9079888 0.4482474 0.1723238
0.4424002 0.0505248 0.8693676 0.4458513 0.1733112
1.0568470 0.2084539 0.4674478 0.5050774 0.2448833
1.1172264 0.0030010 0.3176543 0.3872039 0.2537921
0.9710677 0.0010565 0.3546514 0.4745322 0.2077183
1.1393856 0.1220468 0.4024654 0.3484362 0.1686139
1.0648694 0.1405077 0.4817628 0.4748571 0.1826433
0.8761173 0.0738140 1.0582917 0.7303661 0.0536562
1.2059661 0.1534070 0.7608608 0.6558457 0.1577311
1.0006755 0.0789863 0.8036309 0.8389751 0.0883061

In the genes files, we provide the column headers for the expression matrix in order:

G1
G2
G3
G4
G5

With that, we can run Narromi:

narromi -i expr_mat.tsv -g genes.txt

The output is a square matrix of scores:

0           0           0.581267    0.00822935  0.0106747
0.100319    0           0.00249005  0.0137571   9.62593e-05
0.116941    0.00249005  0           0.624368    0
0.00822935  0.0137571   0.50236     0           0
0.0106747   9.62593e-05 0.29456     0.199657    0

Optional arguments for Narromi

  • -a, --alpha: Initial cutoff for MI selection (alpha).
  • -m, --algorithm: Linear programming algorithm. Interior point is probably faster, but can be unstable for some datasets. When in doubt, choose simplex.

Running Narromi for a subset of genes

Often we have only a small number of genes of interest. We can instruct Narromi to only calculate interactions involving those genes by providing a -t, --targets file containing these gene names:

G3
G4

And running it with the -t, --targets options:

narromi -i expr_mat.tsv -g genes.txt -t targets.txt

In this case we will receive an edge list as output:

G3  G1  0.116941
G3  G2  0.00249005
G3  G4  0.624368
G3  G5  0
G4  G1  0.00822935
G4  G2  0.0137571
G4  G3  0.50236
G4  G5  0

Running Narromi in MPI mode

Narromi can use parallel processing. For general info on how to run parallel algorithms in seidr, please see Using multiple processors to infer networks