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clemencyjolly / PCAWG11-Timing_and_Signatures

Code for mutational timing of gains and signatures analysis
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Example data? #1

Open wjaratlerdsiri opened 3 years ago

wjaratlerdsiri commented 3 years ago

Dear Developer,

I am interested in using both mutational timing of gains and signatures. but I couldn't find any example data to help format my real data. I did try to grab in your Nature publication, but so far unsuccessfully due to its controlled category.

Any test data or examples would be appreciated. VCF and CN formats would be standard, but the requirement of a clustering file is lacking.

Many thanks, James

Se-Jung-LEE commented 2 months ago

Has this issue been resolved by any chance? I'm struggling with the same issue.

In the source code, "#these are all files available for the clustering"

clustering_output_files = list.files(clustering_output_path, pattern = "cluster_assignments.txt.gz", recursive=FALSE, full.names = TRUE)
subclonal_structure_files = list.files(clustering_output_path, pattern = "subclonal_structure.txt.gz", recursive=FALSE, full.names = TRUE)
Se-Jung-LEE commented 2 months ago

I think I found something about our question, so I'm sharing it with you. Maybe you can do something with the output file that comes out of https://github.com/PCAWG-11/Heterogeneity, it would be good for reference.