find_modules {CEMiTool} | R Documentation |
Defines co-expression modules
find_modules(cem, ...) ## S4 method for signature 'CEMiTool' find_modules(cem, cor_method = c("pearson", "spearman"), cor_function = "cor", eps = 0.1, set_beta = NULL, force_beta = FALSE, min_ngen = 20, merge_similar = TRUE, network_type = "unsigned", tom_type = "signed", diss_thresh = 0.8, verbose = FALSE)
cem |
Object of class |
... |
Optional parameters. |
cor_method |
A character string indicating which correlation coefficient
is to be computed. Default |
cor_function |
A character string indicating the correlation function to be used. Default |
eps |
A value for accepted R-squared interval between subsequent beta values. Default is 0.1. |
set_beta |
A value to override the automatically selected beta value. Default is NULL. |
force_beta |
Whether or not to automatically force a beta value based on number of samples. Default is FALSE. |
min_ngen |
Minimal number of genes per submodule. Default |
merge_similar |
Logical. If |
network_type |
A character string indicating to use either "unsigned" (default) or "signed" networks. Default |
tom_type |
A character string indicating to use either "unsigned" or "signed" (default) TOM similarity measure. |
diss_thresh |
Module merging correlation threshold for eigengene similarity.
Default |
verbose |
Logical. If |
Object of class CEMiTool
# Get example expression data data(expr0) # Initialize CEMiTool object with expression cem <- new_cem(expr0) # Filter data cem <- filter_expr(cem) # Define network modules cem <- find_modules(cem) # Check results head(module_genes(cem))