process_network_microbe: process_network_microbe

View source: R/steps.R

process_network_microbeR Documentation

process_network_microbe

Description

Process the network from BugSigDB.

Usage

process_network_microbe(
  ret,
  delete_zero_degree = TRUE,
  make_upper = NULL,
  disease_plot = FALSE,
  ec_plot = FALSE,
  metab = NULL,
  metab_col = NULL,
  metab_thresh = 0.2,
  mb_plot = FALSE,
  ec_file = NULL,
  up_tax_file = NULL
)

Arguments

ret

biotext class object

delete_zero_degree

exclude zero degree nodes from plotting

make_upper

make these words to uppercase

disease_plot

disease plotting

ec_plot

enzyme plotting

metab

metabolite data.frame

metab_col

metabolite data frame column name in the order of "candidate taxon", "metabolite", "quantitative values for thresholding"

metab_thresh

threshold of association in metabolites - taxa relationship (e.g., correlation coefficient)

mb_plot

microbe plotting

ec_file

enzyme database file

up_tax_file

UniProt taxonomy file

Details

Perform tasks before plotting for the data from BugSigDB, like obtaining associated diseases to plot

Value

biotext class object

Examples

## Not run: 
    bugsigdb("Veillonella dispar") |> process_network_microbe()

## End(Not run)

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.