使用NMF进行聚类

安装包

• conda activate wgcna
• conda install -c conda-forge r-nmf -y

确定秩

library(NMF)
dat <- readRDS('PRAD.rds')
res <- nmf(dat,2:7,nrun=10, seed=123)
pdf(file = 'nmf_sp.pdf', width = 12, height = 12);plot(res);dev.off()

绘制共识网络并提取分组

res.3 <- nmf(dat,3,nrun=10, seed=123)
pdf(file = 'nmf_consensusmap.pdf', width = 6, height = 6);consensusmap(res.3);dev.off()
group <- predict(res.3)
group <- as.data.frame(group)
saveRDS(group, 'group.rds')