get_asso_net {PFP} | R Documentation |
This function will remove the co-expressed edges in edges_coexp which also emerge in edges_kegg.
get_asso_net( edges_coexp, edges_kegg, file_dir = NULL, if_symbol = TRUE, trans_fun = trans_edges_id, from_type = "ENTREZID", to_type = "SYMBOL", gene_info_db = NULL )
edges_coexp, |
a data.frame whose colnames is "source","target", "weight","pathway","edge_type". |
edges_kegg, |
a data.frame whose colnames is "source","target", "weight","pathway","edge_type". |
file_dir, |
a character, the root to save the result of nodes & edges. |
if_symbol, |
a logical,whether to translate the gene id type. Default is TRUE. |
trans_fun, |
a function, when |
from_type, |
a character,the parameter in |
to_type, |
a character,the parameter in |
gene_info_db, |
an AnnotationDb-object for gene annotation, such as "org.Hs.eg.db". |
This function will remove the co-expressed edges in edges_coexp which also emerge in edges_kegg. It will return a list contains two data.frames. One is the merged data. Another is the nodes information of the edges.
the nodes information of the edges.
data(PFPRefnet_hsa) data(data_std) data(PFP_test1) rank1 <- rank_PFP(object = PFP_test1,total_rank = TRUE) pathway_select <- refnet_info(rank1)[1,"id"] gene_test <- pathways_score(rank1)$genes_score[[pathway_select]]$ENTREZID edges_coexp <- get_exp_cor_edges(gene_test,data_std) gene_list2 <- unique(c(edges_coexp$source,edges_coexp$target)) edges_kegg <- get_bg_related_kegg(gene_list2, PFPRefnet=PFPRefnet_hsa, rm_duplicated = TRUE)