process_network_gene: process_network_gene

In noriakis/wcGeneSummary: visualization and interpretation of textual information from omics summary data through network analysis

process_network_gene

Description

Process the network from refseq, pubmed or alliance.

Usage

process_network_gene(
  ret,
  delete_zero_degree = TRUE,
  make_upper = NULL,
  make_upper_gene = TRUE,
  org_db = org.Hs.eg.db,
  gene_plot = FALSE,
  gene_plot_num = 5,
  gene_path_plot = NULL,
  gene_path_plot_threshold = 0.05,
  distinguish_query = FALSE
)

Arguments

ret	biotext class object
delete_zero_degree	exclude zero degree nodes from plotting
make_upper	make these words to uppercase
make_upper_gene	make gene symbol to uppercase
org_db	organism database to convert IDs
gene_plot	plot and return associated genes
gene_plot_num	how many genes are to be plotted
gene_path_plot	plot associated pathways related to genes
gene_path_plot_threshold	threshold for pathway enrichment
distinguish_query	distinguish query with words in obtained text

Details

Perform tasks before plotting the networks like obtaining associated genes to plot.

Value

biotext class object

Examples

testgenes <- c("IRF3","PNKP","DDX41","ERCC1","ERCC2","XRCC1")
refseq(testgenes) |>
process_network_gene()

noriakis/wcGeneSummary documentation built on April 22, 2024, 7:12 a.m.