Request for R Code for TCGA Association Analysis Features in Xena hiplot

[quiquemedina]

Dear @ShixiangWang ,

I am following up on my request from two weeks ago regarding the R code for the new features in TCGA Association analysis, specifically those enabling queries of CpG sites and gene coordinates (hg38) within the Xena hiplot platform.

I apologize if my repeated inquiries seem excessive. However, I have been unable to locate the relevant code in the GitHub repository UCSCXenaShiny for use in R.

Could you kindly guide me to the specific location or path where this code can be found?

To illustrate my requirement, I am particularly interested in the process for querying CpG sites associated with the RCAN2 gene in Esophageal Carcinoma (ESCA). The steps I am referring to are as follows:

TCGA Association Analysis
S1 Preset:
a. Select cancer type: ESCA
b. Choose modified dataset:
i. TOIL-DNA Methylation
ii. 450k
iii. Gene: RCAN2
iv. Specify minimum and maximun coordinates to delimit CpG sites:

1. 46391143
2. 46472267
   c. Include 3 CpG sites
   S2 Get Data:
   a. Query data
   b. Define molecular profile:
   i. Methylation
   ii. Identifier: RCAN2
   c. Further data query:
   i. Tumor index
   ii. Tumor stemness
   iii. Identifiers: RNAss
   S3 Analysis & Visualize:
   a. Perform Correlation analysis (Spearman)
   Your assistance with this matter would be greatly appreciated. Thank you for your understanding and support.

Best regards,

Enrique

[ShixiangWang]

@quiquemedina Thanks for your good points as always. @lishensuo has given our initial response in the #257 (comment). We have considered this. However, the server logic and shiny modules have not been split into different parts. We need some time to implement different functions and combine them to serve features directly with R functions. Thanks for your query and patience.