wqhf / igsea

Wrap code for runing GSEA analysis

Bioinformatics_Tools

GSEA analysis on DESeq2 results (Future Plan: Name conversion, database query, ...)

Quick Start

0. Download this package on your machine.

1. You can run the examples now:

   • Example 1. - 'Run_gsea_ex1.r' This example is designed to demonstrate how to run gsea analysis on the input DESeq2 result files ('.csv') that are all put in the same directory.

   • Example 2. - 'Run_gsea_ex2.r' This example is designed to demonstrate how to run gsea analysis on the input DESeq2 object: a '.rda' file

2. To get start on your own dataset, you need to:

   • a) create a /subfolder inside the /Data and copy your DESeq2 files to the /Data/subfolder folder.
   • b) setting the parameters in the section of 'Setting Parameter' (see the details in the above two examples).
   • c) Note that, the GSEA has abundant human gene sets (and a few sets of mouse genes). Thus, we encourge users to convert their transcript IDs to 'human gene names' (see below for the ID mapping procedures).

3. ID conversion: to sucessfully use this package, there are two ways:

   • a) users need to have their DESeq2 results contain a column named "gene_name" to indicate the human gene name for your transcript.
   • b) users can also provide an IDmapping file and assign it to the parameter "IDmappingfile" in your own script, by which our program will automatically convert your transcript ID to human gene name (please see the Tutorial "Tutorial on obtaining IDmapping file.pdf" for obtaining an ID-mapping file).