Processing your own data

You can process your own data in one of two ways.

1) The easy way

Once the app has popped up in your browser, select 'Load my own data' from the sample type menu. So long as the prerequisites are installed, Shiny CGH should upload and process your data for you.

Please note that the data needs to be in TCGA .seg format eg:

TCGA-2F-A9KO 10 109253175 110905211 1027 -0.4865
TCGA-2F-A9KO 10 110905277 111763498 472 -0.1705
TCGA-2F-A9KO 10 111766601 113507257 1194 -0.4592
TCGA-2F-A9KO 10 113514382 135225087 14112 -0.164
TCGA-2F-A9KO 10 39045746 78060379 18548 -0.1608
TCGA-2F-A9KO 10 415240 7943518 5119 0.223
TCGA-2F-A9KO 10 78060510 78162551 88 -0.4986
TCGA-2F-A9KO 10 78168852 109253068 19243 -0.1641
TCGA-2F-A9KO 10 7948874 8058401 72 -0.1798

If you choose this method, then you'll need to re-upload the data every time you use Shiny CGH.

2) The hard way

If you want to preprocess the data, save it as a .Rdata file and permanantly add it to your own Shiny CGH instance, then preprocessing scripts are provided.

i) Navigate to the preprocessing directory.
ii) Place your .seg file(s) in the same directory.
iii) Run the process_CN_files.R script. This should produce two .Rdata files, one for standard gene discovery and one for survival analysis.
iv) Edit the ui.R to point to the new Rdata file:

"Acute Myeloid Leukemia [LAML] TCGA Dec 2014" = "data/LAML.renamed.filtered.seg.standard.Rdata"

v) If you have survival data, you need to add it to the Shiny_CGH_Survival/data/ALL_PATIENT_SURVIVAL.edited.txt file making sure that the patient names in the Rdata file and the survival data file match exactly. Survival data is should be in the following format:

bcr_patient_barcode days_to_last_followup days_to_death
TCGA-ER-A19E 396 396
TCGA-AB-2874 396 [Not Applicable]
TCGA-D1-A16O 865 [Not Applicable]
TCGA-27-1836 914 914