knitr::opts_chunk$set(collapse = TRUE, dev = "png", fig.width = 7, fig.height = 5, message = FALSE, warning = FALSE)
Characterize the stoichiometric reactions of a metabolic model is a required and time-consuming work. The MINVAL package includes the characterizeReactions
function to characterize the stoichiometric functions and metabolites by compartment.
To load the MINVAL package just type:
library(minval)
To show the potential use of the characterizeReactions
function of the MINVAL package the Human Metabolic Reconstruction (RECON 2.04) was included in a human-readable format. To load it just type:
RECON <- read.csv(system.file("extdata", "rRECON2.csv", package = "minval")) dim(RECON)
The characterizeReactions
function requires a set of stoichiometric reactions as input. The given stoichiometric reactions must have the following mandatory characteristics:
'=>'
or '<=>'
(Inverse arrow symbols '<='
or other types as: '-->'
, '<==>'
, '->'
will not be parsed and will lead to errors.)+
) must be surrounded by a space character.-
) symbol.[compartment]
) joined at the end of metabolite name.The characterizeReactions
function:
- Counts the number of reactions
- Computes the relative frequency of each reaction type (transport, exchange and compartmentalized)
- Computes the relative frequency of reactions by compartment
- Counts the number of unique metabolites
- Computes the relative frequency of metabolites by compartment
Finally the characterizeReactions
function returns all these information as a labeled list. To characterize a set of stoichiometric reactions just type:
RECONcharacteristics <- characterizeReactions(reactionList = RECON$REACTION) RECONcharacteristics
Computed values can be easy plotted as follows:
compartmentNames <- c(c = "Cytosol", e = "Extracellular", g = "Golgi apparatus", l = "Lysosome", m = "Mitochondria", n = "Nucleus", r = "Endoplasmic reticulum", x = "Peroxisome" )
Metabolic models generally includes three types of reactions:
h[m] + nadph[m] + o2[m] + 25hvitd2[m] => h2o[m] + nadp[m] + 1a25dhvitd2[m]
2 hco3[e] + na1[e] <=> 2 hco3[c] + na1[c]
acetone[e] <=>
To plot it just type:
pie(x = RECONcharacteristics$rType, main = "Reactions by Type" )
Compartmentalized reactions identified also are categorized and reported as a relative frequency to their associated compartment. To plot it just type:
pie(x = RECONcharacteristics$cReaction, main = "Reactions by Compartment", labels = compartmentNames )
Metabolites are categorized and reported as a relative frequency to their associated compartment. To plot it just type:
pie(x = RECONcharacteristics$cMetabolites, main = "Metabolites by Compartment", labels = compartmentNames )
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