compl_data {famat} | R Documentation

## Data preparation for Shiny interface

### Description

Complete and prepare data obtained with `interactions` function, to use it in the Shiny interface. GO terms enrichment analysis is performed using clusterProfiler.

### Usage

        compl_data(listparam)

### Arguments

`listparam` | Output from `interactions` function

### Value

A list containing :

`heatmap` | Dataframe heatmap-like, with in abscissa elements of pathways ("X" is written if an element is present in a pathway), and with in ordinate hierarchies of pathways
`meta_list` | User's metabolites given in `path_enrich` function
`allResBP` | Results of Go BP terms enrichment analysis performed by clusterProfileR (20 best)
`go_genelist` | Dataframe containing enriched GO terms per genes of user's list
`allResMF` | Results of Go MF terms enrichment analysis performed by clusterProfileR (20 best)
`types` | Dataframe containing categories of pathways per pathways
`genetype` | List of genes categories, containing genes of user's list
`metatab` | Dataframe of metabolites and informations about them, as names and chebi ids
`genetab` | Dataframe of genes and informations about them, as gene symbols and names
`intetab` | Dataframe of direct interactions between elements of user's list, and informations about them as elements in the interaction, how they interact, and which pathways are concerned
`gomf_tab` | Dataframe of Go MF terms hierarchies containing our enriched GO terms, plus description of these GO terms and genes of user's list concerned by enriched GO terms
`gobp_tab` | Dataframe of Go BP terms hierarchies containing our enriched GO terms, plus description of these GO terms and genes of user's list concerned by enriched GO terms
`gene_list` | User's genes given in `path_enrich` function
`gomflist` | List containing GO MF terms hierarchies, with indices in the joliMF dataframe and genes concerned by the hierarchie
`gobplist` | List containing GO BP terms hierarchies, with indices in the joliMF dataframe and genes concerned by the hierarchy
`hierabrite` | List of pathways categories, containing pathways concerned by a category and their indices in "trait" dataframe
`hierapath` | List of hierarchies of pathways, containing indices of pathways in "trait" dataframe and elements contained in the hierarchy.
`save_cluster_elem` | Vector of clustered elements
`centrality` | Matrix trait-like with values of centralities (number of direct interactions between an element of user's list and other elements of the pathway) instead of "X"
`inter_values` | Matrix trait-like with values representing direct interactions (3/2/1, respectively for genes/metabolites implicated in a direct interaction, and for elements not implicated in a direct interaction) instead of "X"
`gene_notin` | Dataframe of genes which aren't in pathways and informations about them, as gene symbols and names
`sub` | Matrix trait-like with pathway and element informations instead of "X"

This list is used by `rshiny` function.

### Author(s)

Emilie Secherre emisecherre@gmail.com

### References

Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology 2012, 16(5):284-287

### See Also

`interactions` `rshiny`

### Examples

        ## load example data
        data(interactions_result)

        compl_data_result=compl_data(interactions_result)

[Package famat version 1.4.0 Index]