process_network_gene: process_network_gene

View source: R/steps.R

process_network_geneR Documentation

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 May 31, 2024, 4:42 p.m.