compound_tbl_lipidblast: Extract compound data from LipidBlast

In EuracBiomedicalResearch/CompoundDb: Creating and Using (Chemical) Compound Annotation Databases

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

EuracBiomedicalResearch/CompoundDb documentation built on Dec. 18, 2024, 4:43 p.m.