The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.
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The R implementation for the Grammar of Succint Lipid Nomenclature parses different shorthand notation dialects for lipid names, normalizes them, and calculates chemical properties.
library(rgoslin)
# Check which grammars are supported
listAvailableGrammars()
# Check whether a given lipid name can be parsed
isValidLipidName("PC 32:1")
# Parse a single lipid name to return a data frame of properties
df <- parseLipidNames("PC 32:1")
# Parse a lipid name with a manually specified grammar
tagDf <- parseLipidNames("TG(16:1(5E)/18:0/20:2(3Z,6Z))", grammar = "LipidMaps")
# Parse multiple lipid names using a vector
multipleLipidNamesDf <- parseLipidNames(c("PC 32:1", "LPC 34:1", "TG(18:1_18:0_16:1)"))
Input: A character vector of lipid shorthand names. Output: A data frame containing parsed lipid properties (e.g., normalized name, mass, sum formula, category).
parseLipidNames().isValidLipidName().parseLipidNames(..., grammar = "FattyAcids").xcms instead.MSnbase or Spectra instead."PC 32:1", "TG(16:1(5E)/18:0/20:2(3Z,6Z))")."Shorthand2020", "Goslin", "FattyAcids", "LipidMaps", "SwissLipids", and "HMDB"."Goslin", "LipidMaps", "FattyAcids"). If omitted, all available parsers are tested sequentially.listAvailableGrammars() to check supported grammars before parsing.grammar parameter in parseLipidNames() when parsing large vectors to avoid testing all parsers and improve performance.isValidLipidName() to quickly filter out unparseable names before running full parsing.grammar argument on large datasets: Causes slow execution because all grammars are tested sequentially. Fix: Specify grammar = "Goslin" or another specific grammar.(d9)): Causes parsing errors. Fix: Preprocess names using string manipulation (e.g., str_match or str_replace_all) to remove or convert suffixes before parsing.lipidr: For downstream analysis, visualization, and QC of lipidomics data (can be integrated with rgoslin).MSnbase: For low-level mass spectrometry data container handling.Spectra: For raw mass spectra representation and processing.まだレビューはありません。使ってみた感想をお寄せください。
概要と使いどころ
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