compl_data_result: Output of 'compl_data' function
In emiliesecherre/famat: Functional analysis of metabolic and transcriptomic data

compl_data_result

R Documentation

Output of `compl_data` function

Description

Enriched and structured informations about genes, metabolites, their interactions, pathways and enriched GO terms.

Usage

data("compl_data_result")

Format

List of 22 items.

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. A data frame with 16 rows and 9 variables.

path_name: Hierarchies of pathways obtained by pathways enrichment analysis. Pathways are given by their name.
path_id: Identifiers of pathways in hierarchies.
meta_ratio: Metabolites ratio, so the part of user's metabolites in the total number of metabolites in the pathway.
gene_ratio: Genes ratio, so the part of user's genes in the total number of genes in the pathway.
blank: Just an empty column to separate heatmap data from pathways data (NA).
SLC6A12: The value "1" shows that the element SLC6A12 is in the pathway on the row, "0" shows it is not in this pathway (0–1).
Betaine: The value "1" shows that the element Betaine is in the pathway on the row, "0" shows it is not in this pathway (0–1).
ATP: The value "1" shows that the element ATP is in the pathway on the row, "0" shows it is not in this pathway (0–1).
Betaine / SLC6A12: The value "1" shows that the interaction Betaine / SLC6A12 is in the pathway on the row, "0" shows it is not in this pathway (0–1).

meta_list

Vector containing user's metabolites (C00002, C00719)

allResBP

Results of Go BP terms enrichment analysis performed by clusterProfileR (20 best). A data frame with 20 rows and 9 variables.

ID: Identifiers of enriched GO terms.
Description: Names of enriched GO terms.
GeneRatio: Number of user's genes concerned by the enriched GO term, by total number of user's genes.
BgRatio: Number of genes concerned by the enriched GO term, by the total number of annotated genes in the database.
pvalue: Pvalue of the go term enrichment analysis (0.001392161–0.011536208).
p.adjust: Adjusted pvalue of the go term enrichment analysis (0.01713291–0.02670275).
qvalue: Qvalue of the go term enrichment analysis (0.001803464–0.002810816).
geneID: Entrez Gene identifiers of all genes concerned by the enriched GO term (30, 6539).
Count: Number of genes concerned by the enriched GO term described by an Entrez Gene identifier(1).

go_genelist

Dataframe containing enriched GO terms per genes of user's list. A data frame with 13 rows and 2 variables.

hgnc_symbol: Gene symbol of the gene concerned by an enriched GO term (SLC6A12, ACAA1).
go_id: Identifier of the GO term concerning the gene (GO:0005328, GO:0015293, GO:0003333, GO:0015812, GO:0015171, GO:0042165, GO:0008028, GO:0006635, GO:0006625, GO:0033540, GO:0036109, GO:0008206, GO:0000038)

allResMF

Results of Go MF terms enrichment analysis performed by clusterProfileR (20 best) A data frame with 20 rows and 9 variables.

ID: Identifiers of enriched GO terms.
Description: Names of enriched GO terms.
GeneRatio: Number of user's genes concerned by the enriched GO term, by total number of user's genes.
BgRatio: Number of genes concerned by the enriched GO term, by the total number of annotated genes in the database.
pvalue: Pvalue of the go term enrichment analysis (0.001392161–0.011536208).
p.adjust: Adjusted pvalue of the go term enrichment analysis (0.01713291–0.02670275).
qvalue: Qvalue of the go term enrichment analysis (0.001803464–0.002810816).
geneID: Entrez Gene identifiers of all genes concerned by the enriched GO term (30, 6539).
Count: Number of genes concerned by the enriched GO term described by an Entrez Gene identifier(1).

types

Dataframe containing categories of pathways per pathways. A data frame with 12 rows and 2 variables.

id: Identifier of pathways from pathways enrichment analysis.
root: Name of the pathway category concerning a pathway.

genetype

List of genes categories, containing genes of user's list. A list of 3 items.

metatab

Dataframe of metabolites and informations about them, as names and chebi ids. A data frame with 2 rows and 2 variables.

id: Name of user's metabolites (ATP, Betaine).
name: Chebi identifier of user's metabolites (CHEBI:15422, CHEBI:17750).

genetab

Dataframe of genes and informations about them, as gene symbols and names. A data frame with 1 rows and 2 variables.

id: Gene symbols of user's genes contained in pathways (SLC6A12).
name: Name of user's genes contained in pathways (solute carrier family 6 member 12).

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 A data frame with 1 row and 8 variables.

tag: Summary of elements concerned by the interaction (Betaine / SLC6A12)
first_item: First element of the direct interaction (Betaine)
link: Description of how the two elements interact (Control(In: ACTIVATION of BiochemicalReaction), controls-transport-of-chemical).
sec_item: Second element of the direct interaction (SLC6A12)
go: Value "1" means that a gene of the interaction is concerned by an enriched GO term, "0" means no element is concerned by an enriched GO term (1).
path: Pathways containing the direct interaction ("R-HSA-112310, R-HSA-112315, R-HSA-112316, R-HSA-382551, R-HSA-425366, R-HSA-425393, R-HSA-425407, R-HSA-888590, R-HSA-352230, R-HSA-442660, R-HSA-888593")
type: Interaction type, can be gene/gene, metabolite/metabolite, or gene/metabolite (g/m)
cat: Categories of pathways containing the direct interaction (Neuronal System, Transport of small molecules)

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. A data frame with 93 rows and 3 variables.

goterm: Hierarchies of enriched GO terms.
go_name: Names of GO terms.
genes: Genes concerned by 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. A data frame with 107 rows and 3 variables.

goterm: Hierarchies of enriched GO terms.
go_name: Names of GO terms.
genes: Genes concerned by GO terms.

gene_list

Vector containing user's genes (ACAA1, SLC6A12)

gomflist

List containing GO MF terms hierarchies, with indices in the joliMF dataframe and genes concerned by the hierarchie. A list of 3 items.

gobplist

List containing GO BP terms hierarchies, with indices in the joliMF dataframe and genes concerned by the hierarchy. A list of 5 items.

hierabrite

List of pathways categories, containing pathways concerned by a category and their indices in "trait" dataframe. A list of 3 items.

hierapath

List of hierarchies of pathways, containing indices of pathways in "trait" dataframe and elements contained in the hierarchy. A list of 3 items.

save_cluster_elem

Vector of clustered elements

centrality

Matrix heatmap-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". Other cells contain the value "0" (0–65). An integer matrix with 16 rows and 9 columns.

inter_values

Matrix heatmap-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". Other cells contain the value "0" (0–3). An integer matrix with 16 rows and 9 columns.

gene_notin

Dataframe of genes which aren't in pathways and informations about them, as gene symbols and names. A data frame with 1 row and 2 variables.

id: Gene symbols of genes (ACAA1).
name: Names of genes (acetyl-CoA acyltransferase 1).

sub

Matrix heatmap-like with pathway and element informations instead of "X". Cells with no informations contain only "". A character matrix with 16 rows and 9 columns.