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.
After GISTIC each genomic region has a copy-number assigned (or before GISTIC, does not matter much). You may measure distances between different samples as Manhattan distance for each elementary genomic region. Thus, you may measure distances between all the pairs of your samples. Then you can perform hclust in R, using the resulting matrix of distances.