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dshcherbo / cfDNA-FEP

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How to get Supplementary Fig.1 #2

Closed EarnestJJ closed 2 years ago

EarnestJJ commented 2 years ago

Dear Dr. Shcherbo Recently,I read your article, it is a interesting job. When i tried to reproduce the Supplementary Fig.1, I couldn't get similar results according to description of article(The original description from article：we selected 48 COAD-specific and 48 RCC-specific peaks based on their normalized scores and specificity for the corresponding cancer type). I think my method is not appropriate or my understanding is not correct. I hope you can provide this part of the code. Thank you very much.

dshcherbo commented 2 years ago

Dear @EarnestJJ Thank you for your interest. The Supplementary Figure 1 is based on the TCGA ATAC-seq data from Corces et al 2018, not on the data generated in our study. You can get the dataset here (the rds file under the title Normalized ATAC-seq insertion counts within the pan-cancer peak set) and visualize genomic regions that we studied (the ids of the peaks are listed in the 00-all_primers.bed file) as a heatmap. I hope this helps.

EarnestJJ commented 2 years ago

@dshcherbo Thank you for your reply, This is very helpful to me. But I have another question which is for example if I want to find out LUAD-specific peaks, as we know the rds File has a lot of peaks of LUAD,so I can pick out peaks of LUAD firstly, then how do I screen out the LUAD-specific peaks based on normalized scores and specificity(As described in your article, I don't konw how to screen specific peaks according to these two criteria). Looking forward to your reply, Thanks a lot.

dshcherbo commented 2 years ago

@EarnestJJ We did not implement any automated algorithm to select the peaks. This was done manually for each cancer (with visualization and inspection in Xena Browser where the dataset is preloaded) after filtering out regions that were present in other cancers.