build.bio.connectivity.matrix: Building Biotransformations connectivity matrix

In francescodc87/IPA: Integrated Probabilistic Annotation (IPA) method for mass spectrometry data

Building Biotransformations connectivity matrix

Description

This functions created the Biotransformations connectivity matrix needed for the posterior estimation

Usage

build.bio.connectivity.matrix(Prior, DB, ionisation,
  connection.type = "reactions", connections = NULL, v = TRUE,
  IT = 500)

Arguments

Prior	The output of compute.Priors() function
DB	The database used in a dataframe format. It has to be organized in the same fashion of the one included with the package
ionisation	A character indicating the ionisation mode of the experiment, either 'positive' or 'negative'
connection.type	if equal to "reactions" (default) considers the reactions reported in the database. If it is equal to "formulas", the function consider the list of possible reactions reported in connections
connections	if connection.type=="fomulas", this vector contains a list of formulas that are likely to be added or substracted by an enzymatic reaction. If it is equal to NULL the default list of formulas is used
v	A logical value indicating if the progress will be shown (default TRUE)
IT	A number inticating after how many iteration an update should be shown (default 500)

Value

A binary matrix encoding the biotransfiormations connections

Author(s)

Francesco Del Carratore [e-mail]

See Also

build.add.connectivity.matrix build.iso.connectivity.matrix

francescodc87/IPA documentation built on April 7, 2023, 4:27 a.m.