load data
MGH136 = readRDS(‘data/MGH136.rds’)
1: Center expression matrix
MGH136.cent = scalop::rowcenter(MGH136)
… Using scalop::programs …
2: Generate an ordered correlation matrix
3: Retrieve cell clusters with NO CUTOFF. This is the real step
3!
4: Define gene programs from each cell cluster
5i: Remove not-significant programs
5ii: Remove too-redundant clusters/programs
prog_obj = scalop::programs(MGH136.cent, lfc = log2(2), pmethod =
‘BH’, p = 0.01, nsig1 = 50, jaccard = 0.7)
25 clusters
lengths(prog_obj)
cluster 1: CC?
prog_obj\(groups[[1]]
prog_obj\)profiles[[1]] %>% head prog_obj\(profiles[[1]] %>% length
prog_obj\)programs[[1]]
cluster 10: MES?
prog_obj\(groups[[10]]
prog_obj\)profiles[[10]] %>% head prog_obj\(profiles[[10]] %>% length
prog_obj\)programs[[10]]