compl_data_result {famat} | 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.

### Source

`compl_data` function

[Package famat version 1.0.0 Index]