cem_overlap {CEMiTool} | R Documentation |
Returns the occurrence of edges between different analyses
cem_overlap(..., analyses_list = NULL, fraction = 1)
... |
Objects of class |
analyses_list |
List of objects of class |
fraction |
The fraction of objects in which an edge pair must be present to be selected (default = 1, accepts values from 0-1) |
The method assumes that all genes inside each module are connected to every other gene from the same module.
Object of class data.frame
containing edgelist describing common
edges between the networks defined in module slots from the input objects
## Not run: # Run cemitool twice on expr dataset. In each time, one sample will be removed data(expr0) set.seed(10) dset1 <- expr0[,-sample(1:ncol(expr0), 1)] dset2 <- expr0[,-sample(1:ncol(expr0), 1)] cem1 <- cemitool(dset1) cem2 <- cemitool(dset2) cemoverlap_df <- cem_overlap(cem1, cem2) # Can also be run with a list: cemoverlap_df <- cemoverlap(list(cem1, cem2)) # Different types of objects can be combined as well, and invalid objects will be removed, with a warning cemoverlap_df <- cem_overlap(cem1, cem2, module_genes(cem), NA, 1, NULL) ## End(Not run)