Meta2pathway: Meta2pathway
In BiOFI: Feature Identification Between Metabolome and Microbiome in Disease and Health
Meta2pathway R Documentation
Meta2pathway
Description
A function is used to predict the metabolic functional pathways according to the abundance of metabolites based on the algorithm Pathway Activity Profiling (PAPi).
Note: Please use compound IDs in KEGG database to replace the names of metabolites. For example, C00002 means ATP or Adenosine 5'-triphosphate in KEGG.
Users also can use Metaboanalyst (https://www.metaboanalyst.ca/MetaboAnalyst/upload/ConvertView.xhtml)(Pang, et al., 2022) to convert the metabolites names to compound IDs.
If metabolites do not have compound IDs, keep the original names.
See data example "Meta2pathway.eg" for details.
Usage
Meta2pathway(metadf)
Arguments
metadf
A data frame including metabolites with compound ID and abundance.
Value
meta2path_res A data frame containing metabolites with compound ID and predicted KEGG pathways.
Examples
Meta2pathway_res <- Meta2pathway(metadf = Meta2pathway.eg)
BiOFI documentation built on Sept. 22, 2022, 9:07 a.m.
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| Meta2pathway | R Documentation |
Meta2pathway
Description
A function is used to predict the metabolic functional pathways according to the abundance of metabolites based on the algorithm Pathway Activity Profiling (PAPi). Note: Please use compound IDs in KEGG database to replace the names of metabolites. For example, C00002 means ATP or Adenosine 5'-triphosphate in KEGG. Users also can use Metaboanalyst (https://www.metaboanalyst.ca/MetaboAnalyst/upload/ConvertView.xhtml)(Pang, et al., 2022) to convert the metabolites names to compound IDs. If metabolites do not have compound IDs, keep the original names. See data example "Meta2pathway.eg" for details.
Usage
Meta2pathway(metadf)
Arguments
metadf |
A data frame including metabolites with compound ID and abundance. |
Value
meta2path_res A data frame containing metabolites with compound ID and predicted KEGG pathways.
Examples
Meta2pathway_res <- Meta2pathway(metadf = Meta2pathway.eg)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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