compl_data: Data preparation for Shiny interface

In famat: Functional analysis of metabolic and transcriptomic data

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 [e-mail]

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)

famat documentation built on Nov. 8, 2020, 5:56 p.m.