compound_tbl_lipidblast: Extract compound data from LipidBlast

View source: R/createCompDbPackage.R

compound_tbl_lipidblastR Documentation

Extract compound data from LipidBlast

Description

compound_tbl_lipidblast() extracts basic compound annotations from a LipidBlast file in (json format) downloaded from http://mona.fiehnlab.ucdavis.edu/downloads . Note that no mass spectra data is extracted from the json file.

Usage

compound_tbl_lipidblast(
  file,
  collapse = character(),
  n = -1L,
  verbose = FALSE,
  BPPARAM = bpparam()
)

Arguments

file

character(1) with the name of the file name.

collapse

optional character(1) to be used to collapse multiple values in the columns "synonyms". See examples for details.

n

integer(1) defining the number of rows from the json file that should be read and processed at a time. By default (n = -1L) the complete file is imported and processed. For large json files it is suggested to set e.g. n = 100000 to enable chunk-wise processing and hence reduce the memory demand.

verbose

logical(1) whether some progress information should be provided. Defaults to verbose = FALSE, but for parsing very large files (specifically with chunk-wise processing enabled with n > 0) it might be helpful to set to verbose = TRUE.

BPPARAM

BiocParallelParam object to configure parallel processing. Defaults to bpparam().

Value

A tibble::tibble with general compound information (one row per compound):

  • compound_id: the ID of the compound.

  • name: the compound's name.

  • inchi: the InChI of the compound.

  • inchikey: the InChI key.

  • smiles: the SMILES representation of the compound.

  • formula: the chemical formula.

  • exactmass: the compound's mass.

  • compound_class: the class of the compound.

  • ionization_mode: the ionization mode.

  • precursor_mz: the precursor m/z value.

  • precursor_type: the precursor type.

  • retention_time: the retention time.

  • ccs: the collision cross-section.

  • spectrum: the spectrum data (i.e. the mass peaks, as a concatenated character string).

  • synonyms: the compound's synonyms (aliases). This type of this column is by default a list to support multiple aliases per compound, unless argument collapse is provided, in which case multiple synonyms are pasted into a single element separated by the value of collapse.

Author(s)

Johannes Rainer, Jan Stanstrup and Prateek Arora

See Also

Other compound table creation functions: compound_tbl_sdf()

Examples


## Read compound information from a subset of HMDB
fl <- system.file("json/MoNa-LipidBlast_sub.json", package = "CompoundDb")
cmps <- compound_tbl_lipidblast(fl, n = 50000, verbose = TRUE)
cmps

rformassspectrometry/CompoundDb documentation built on Aug. 1, 2024, 2:33 a.m.