raphael_examples/simple/README.md

In jhrcook/wext: Weighted Exclusivity Test (WExT)

Toy problem example

The commands in sh commands.sh illustrate WExT on a small toy problem. If the dependencies for WExT are correctly installed, then the commands.sh script should run within several seconds on your computer. These commands have three major parts.

1. Process mutation data process_mutations.py
2. Compute mutation weights/probabilities compute_mutation_probabilities.py.
3. Find gene sets with significant patterns of mutually exclusive or co-occurring mutations find_sets.py.

This example applies the WR-exact test for mutual exclusivity and co-occurrence on pairs of genes in a small toy dataset using a saddlepoint approximation of each test. The WExT wiki describes the details of the above tests and the arguments for the above scripts in more detail.

Input

The dataset has 8 genes, a, b, ..., h, and 14 patients, 1, 2, ..., 14, where all mutations in genes a and b are mutually exclusive and all mutations in genes c and d are co-occurring.

1   a   c   d   e   f
2   b   c   d   g   h
3   a   c   d
4   b   c   d
5   a   c   d
6   b   c   d
7   a   c   d
8   b
9   a
10  b
11  a   e
12  b   g
13  c   d
14  c   d

Output

The mutual exclusivity results (exclusivity_results-k2.tsv) should be very similar to the following table, which shows that only genes a and b have mutually exclusive mutations with the (default) FDR < 0.5.

#Gene set   WRE (Saddlepoint) P-value   WRE (Saddlepoint) FDR   WRE (Saddlepoint) Runtime   T   Z   t00 t01 t10 t11
a, b    0.000246182027855   0.0101775930969 0.00236916542053    12  0   2   6   6   0

The co-occurrence results (any-co-occurrence_results-k2.tsv and all-co-occurrence_results-k2.tsv) should be very similar to the following table, which shows that only genes c and d have co-occurring mutations with the (default) FDR < 0.5.

#Gene set   WRE (Saddlepoint) P-value   WRE (Saddlepoint) FDR   WRE (Saddlepoint) Runtime   T   Z   t00 t01 t10 t11
c, d    0.0037414655014 0.186225589558  0.00187397003174    0   9   5   0   0   9

jhrcook/wext documentation built on May 17, 2021, 1:19 a.m.