listk: Pathway enrichment analysis results for KEGG pathways.

In famat: Functional analysis of metabolic and transcriptomic data

Description

Results of pathways enrichment analysis on the list of genes and metabolites, using KEGG pathways. Pathways enrichment analysis is performed using MPINet for metabolites and gprofiler2 for genes.

Usage

data("listk")

Format

A list of 4 items.

resmeta

Pathway enrichment analysis results for metabolites. A data frame with 7 rows and 2 variables.

name

Name of pathways resulting in metabolites pathway enrichment analysis.

id

Identifiers of pathways resulting in metabolites pathway enrichment analysis.

resgene

Pathway enrichment analysis results for genes. A data frame with 11 rows and 2 variables.

name

Name of pathways resulting in genes pathway enrichment analysis.

id

Identifiers of pathways resulting in genes pathway enrichment analysis.

gened

Vector containing user's genes (ACAA1, SLC6A12)

metad

Vector containing user's metabolites (C00002, C00719)

Source

path_enrich function.

References

Yanjun Xu, Chunquan Li and Xia Li (2013). MPINet: The package can implement the network-based metabolite pathway identification of pathways.. R package version 1.0. https://CRAN.R-project.org/package=MPINet

Liis Kolberg and Uku Raudvere (2020). gprofiler2: Interface to the 'g:Profiler' Toolset. R package version 0.2.0. https://CRAN.R-project.org/package=gprofiler2

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