compl_data: Data preparation for Shiny interface

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/compl_data.R

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

1
    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

1
2
3
4

emiliesecherre/famat documentation built on Dec. 1, 2020, 9:34 p.m.