Hi, I got recurrent copy number alteration results using GISTIC 2.0 and now I want to perform hierarchical clustering of copy number data.
I got heatmap from GISTIC, but there's no clustering result. (raw_copy_number.pdf)
I wonder which file I should use to make a new heatmap and perform hierarchical clustering.
Levine, D., The Cancer Genome Atlas Research Network., Genome sequencing centres: Broad Institute. et al. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67–73 (2013). https://doi.org/10.1038/nature12113
I'd like to make a result like a paper I wrote above. (Especially figure 1)
Supplementary methods in the paper: Significant focal copy number alterations were identified from segmented data using GISTIC 2.0. Hierarchical clustering of copy number data was performed using R on threshold relative copy number data in significantly reoccurring amplification or deletions regions identified by GISTIC 2.0 analysis.
Please let me know if know how. Thank you.