get_asso_net: merge the edges_coexp and edges_kegg

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

Description

This function will remove the co-expressed edges in edges_coexp which also emerge in edges_kegg.

Usage

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
)

Arguments

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 if_symbol is TRUE,it will use the trans_fun function to translate the gene ids. Default is trans_edges_id.
from_type,	a character,the parameter in trans_fun. It is the type of gene ID, "ENSEMBL","GO","SYMBOL" and so on.
to_type,	a character,the parameter in trans_fun. It is the type of gene ID, "ENSEMBL","GO","SYMBOL" and so on.
gene_info_db,	an AnnotationDb-object for gene annotation, such as "org.Hs.eg.db".

Details

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.

Value

the nodes information of the edges.

Examples

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)

aib-group/PFP documentation built on Dec. 27, 2020, 1:13 a.m.