get_bg_related_kegg: get_bg_related_kegg
In aib-group/PFP: Pathway Fingerprint Framework in R

Description Usage Arguments Details Value Examples

This function will select all genes in all kegg pathways which are directly connected with the genes in gene_list

1	get_bg_related_kegg(gene_list, PFPRefnet, rm_duplicated = FALSE)

`gene_list,`	a vector of characters, refers to genes ids
`PFPRefnet,`	an object of PFPRefnet class, it contains all kegg pathways.
`rm_duplicated,`	a logical, whether to remove the duplicated kegg edges in different pathways. Defalut is FALSE

It will return a data.frame which can be translated a graph or network. In the data.frame, source refers to the genes in gene_list, target refers to the directly connected genes in kegg, weight is 0.5, no real means, pathwayrefers to the pathway which the edge emerge and edge_type is "kegg".Note, if rm_duplicated is FALSE, it may return many duplicated edges,which will be complex when plotting a network. If rm_duplicated is TRUE,it will retain the first pathway which contains the duplicated edge.

the related kegg network.

data(PFPRefnet_hsa)
data(gene_list_hsa)
edges_kegg <- get_bg_related_kegg(gene_list_hsa,
                                  PFPRefnet=PFPRefnet_hsa,
                                  rm_duplicated = TRUE)