prepare_metabolomics_data {cosmosR} | R Documentation

## format COSMOS metabolic input

### Description

This function prepares the metabolic data to be used in the COSMOS optimization steps. It takes as input a vector with the metabolic data (e.g, limma t values) named with PUBCHEM IDs and expand it to the multi-compartment COSMOS format. It also messages the number of final inputs in the meta network.

### Usage

    prepare_metabolomics_data(metabolic_data, meta_network)

### Arguments

`metabolic_data` | A named numeric vector, containing the values to be used for the metabolic layer in COSMOS. The names of the vector should be PUBCHEM IDs.
`meta_network` | Prior knowledge network created with `data(meta_network)`.

### Value

A new vector ready to be used as COSMOS input.

### Examples

    # generate random t-values:
    t_values <- rnorm(10)
    # assign to metabolites with pubchem names
    data(metabolite_to_pubchem)
    names(t_values) <- names(metabolite_to_pubchem)[1:10]

    data(meta_network)
    prepare_metabolomics_data(t_values, meta_network)

[Package cosmosR version 1.2.0 Index]