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Extracts co-clustered PTM and gene network from a cluster filtered network object.

ptms_to_cfn.Rd

This function takes a list of PTM (post-translational modification) site IDs and a cluster-filtered network, extracts the genes from unambiguous and ambiguous PTM entries, then returns the co-clustered subnetwork.

Usage

ptms_to_cfn(ptms, cfn = cfn.merged, pepsep = ";")

Arguments

ptms

Character vector of PTM site strings (e.g., \"TP53 p S15\")

cfn

List or data frame representing the cluster filtered network (default: global cfn.merged)

pepsep

Character used to split ambiguous PTM entries (default: \";\")

Value

Subnetwork object with co-clustered PTMs and genes

Examples

# Example input objects
ptms <- c("TP53 p S15", "BRCA1 p S123; BRCA1 p T124", "MDM2 p S200")
# Example network
# edge list with 'source', 'target', and cluster info, could be data.frame or igraph
cfn.merged <- data.frame(source = c("TP53", "BRCA1", "BRCA1", "MDM2"),
                         target = c("BRCA1", "MDM2", "TP53", "TP53"),
                         cluster = c(1,1,2,1))
# Suppose filter.edges.0 and get.co.clustered.ptms are also defined and loaded
# The following returns the gene/PTM subnetwork
res <- ptms_to_cfn(ptms, cfn = cfn.merged, pepsep = ";")
#> Error in ptms_to_cfn(ptms, cfn = cfn.merged, pepsep = ";"): object 'cfn.merged' not found
print(res)
#> Error: object 'res' not found