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For the pan-cancer data we can compute 'distances' between the various files. We need these distances to better assess patients activity. See below.

Update the significant genes script to compute these values.

We do not need the full omicsintegrator package. instead we can build out tools to build igraph/networkx/array versions of graphs in a much easier format.

currently the code computes GO enrichment for the individual patients, but not the communities. update the code to compute enrichment for the communities. See pancancer script for example.

Current somatic mutations for MPNST datasets are located in syn22136398. To process these data in a network we first need to pull download the files and collect the per-gene allele depth for each sample. The final data structure will be a dictionary of dictionaries. The primary key will be the specimenID, the internal dictionary will be keyed on gene symbol. the value will be the allele depth.

Downloading a synapse file is straightforward once the package is downloaded.

from synapseclient import Project, File, Folder
from synapseclient import Schema, Column, Table, Row, RowSet, as_table_columns

syn = synapseclient.Synapse()
syn.login()

project = syn.get('syn123')

The results for this will go into the [./examples/mutationDrugResponse] directory for now (we can consider making a synapse utility but i'm not sure about this.

Using the CPTAC patient data, pull the 'LogRatio' column from the molecular table that you accessed in #2 and for each gene, compute the z-score (i.e. (x-mean(x))/sd(x)) so we can assess the relative expression of each gene for each patient. Then create a dictionary of dictonaries - one for each sample, one for each gene/protein value.

This is similar to #1 but might be trickier (or easier) because mutational data for CPTAC is stored in a synapse table. this requires a slightly different syntax to pull the data and put it into a dictionary of dictionaries. The primary key on the dictionaries is the sample identifier, the internal one is the gene symbol.

The table is here: https://www.synapse.org/#!Synapse:syn22172602/tables/