Uses common lipid nomenclature to simplify lipid annotations

Based on rgoslin, this function has the ability to simplify lipid annotations into more general terms, groups and classes. This function can input a data frame containing a column storing the annotation and refine only the entries which are annotated as known lipid structures.

Usage

RefineLipids(
  data,
  annotation.column = "annotations",
  database = "HMDB",
  lipid_info = "simple"
)

Arguments

data

data.frame containing a column with lipid annotations

annotation.column

Character string matching the column name containing the lipid annotations in the provided df (default = "annotations").

database

Character string defining the database matching the lipid annotations. Possible entries include c('Shorthand2020','Goslin','FattyAcids','LipidMaps','SwissLipids','HMDB') (default = "HMDB").

lipid_info

Character string defining what level of information to return for each lipid. Options are either "all" or "simple". "Simple" returns a smaller, simplified list of annotations for each lipid. Please visit https://bioconductor.org/packages/release/bioc/vignettes/rgoslin/inst/doc/introduction.html to see all possible outputs (default = "simple")).

Value

Data.frame containing additional columns with simplified lipid names

Examples

# RefineLipids(DEPs_df)