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.