read_flux: Reads flux data from a file or data frame

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Reads flux data from a file or data frame

Description

Reads flux data from a file or data frame

Usage

read_flux(
  file.data = dat_flux,
  csvsep = ";",
  dec = ".",
  sheet.data = 1,
  file.match = "eq_bigg.csv",
  sheet.match = 1,
  rename.reaction = TRUE,
  rescale.reaction = NULL,
  col.id = "Reaction ID",
  col.eq = "Equation",
  col.flux = "Value (%)",
  col.sd = "Standard Deviation",
  FBA = FALSE
)

Arguments

file.data	Path to the file containing the flux data. Alternatively, a data frame can be provided.
csvsep	Separator used in the file. Default is ";".
dec	Decimal separator used in the file. Default is ".".
sheet.data	Sheet number to read from the file. Default is 1.
file.match	Path to the file containing the equation-BiGG name matches.
sheet.match	Sheet number to read from the file matching equations to BiGG reaction names. Default is 1.
rename.reaction	Logical, whether to rename reactions according to BiGG standard. Default is TRUE.
rescale.reaction	Name of a reaction to normalize all fluxes (will be set as 100%). Default is NULL.
col.id	Name of the column containing reaction IDs. Default is "Reaction ID".
col.eq	Name of the column containing carbon transition equations. Default is "Equation".
col.flux	Name of the column containing flux values. Default is "Value (%)".
col.sd	Name of the column containing standard deviation values. Default is "Standard Deviation".
FBA	Logical, whether the data is from an FBA simulation. Default is FALSE.

Value

A data frame with reaction IDs, equations, flux values, and standard deviation.

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.