Hello,
Thank you for developing this tool and making it open source. I have a question about how Hefree et al. actually identified the subnets mutated in each cluster. In the online methods, it says that the network-smoothed mutational profiles were analyzed with the non-parametric option of SAM. Were the "network-smoothed mutation profiles" produced on a per sample basis (ie. one per sample, starting with a 1 at each mutated node and RWR-smoothing from there), or were the mutational frequencies of the genes in each sample smoothed? In other words, was a network-smoothed mutational profile made for each sample separately, or was one network-smoothed mutational profile made for each cluster (more like HotNet)?
Thank you for any help you can offer,
Josh Cook
Hello,
Thank you for developing this tool and making it open source. I have a question about how Hefree et al. actually identified the subnets mutated in each cluster. In the online methods, it says that the network-smoothed mutational profiles were analyzed with the non-parametric option of SAM. Were the "network-smoothed mutation profiles" produced on a per sample basis (ie. one per sample, starting with a
1at each mutated node and RWR-smoothing from there), or were the mutational frequencies of the genes in each sample smoothed? In other words, was a network-smoothed mutational profile made for each sample separately, or was one network-smoothed mutational profile made for each cluster (more like HotNet)?Thank you for any help you can offer,
Josh Cook