special-guide

Testing the GSVA Package

Data Long Drive Repo

Data in: L:\Richard B\Analysis\2019\May 2019\testing_the_GSVA_package

Richard Trial Data

See the 'rjb_trial' dir. The 'rjb_trial_gsva_script.R' has a very basic explaination of GSVA using some made up data. This shows enrichment in the S2 sample and also a downregulation enrichment in the S3 sample.

GSVA Vignette 4.1 Functional Enrichment Leukaemia Example

Using the vignette example to find functionally enriched gene sets between two phenotypes (ALL and MLL). The '4.1_functional_enrichment' dir. The '4_1_functional_enrichment_script.R' has the 4.1 vignette example as a workthrough to understand it for me.

GSVA Vignette 4.2 Molecular Signature Identification Example

Using the vignette example to use custom defined gene expression signatures to find brain cells. Similar to what I want to do, except not taking sample subtype into account. The '4.2_molecular_signature' dir. The '4_2_molecular_signature_script.R' has the 4.2 vignette example as a workthrough to understand it for me.