get_mods {CEMiTool} | R Documentation |
This function takes a CEMiTool
object containing an adjacency matrix
together with the given network parameters, and returns the given
co-expression modules.
get_mods(cem, ...) ## S4 method for signature 'CEMiTool' get_mods( cem, cor_function = "cor", cor_method = "pearson", tom_type = "signed", min_ngen = 20 )
cem |
Object of class |
... |
Optional parameters. |
cor_function |
A character string indicating the correlation function
to be used. Default |
cor_method |
A character string indicating which correlation
coefficient is to be computed. Default |
tom_type |
A character string indicating to use either "unsigned" or "signed" (default) TOM similarity measure. |
min_ngen |
Minimal number of genes per module (Default: 20). |
Numeric labels assigning genes to modules.
# Get example expression data data(expr0) # Initialize new CEMiTool object with expression data cem <- new_cem(expr0, filter=TRUE, apply_vst=FALSE) # Calculate adjacency matrix with example beta value 8 cem <- get_adj(cem, beta=8) # Get module labels mods <- get_mods(cem)