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Extract compound data from LipidBlast

Source: R/createCompDbPackage.R
compound_tbl_lipidblast.Rd

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.

See also

Other compound table creation functions: compound_tbl_sdf()

Author

Johannes Rainer, Jan Stanstrup and Prateek Arora

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)
#> Processed 1 elements
cmps
#> # A tibble: 8 × 15
#>   compound_id      name   inchi inchikey smiles formula exactmass compound_class
#>   <chr>            <chr>  <chr> <chr>    <chr>  <chr>       <dbl> <chr>         
#> 1 LipidBlast000001 CerP … InCh… FIIUKKI… "CCCC… C24H50…      479. CerP          
#> 2 LipidBlast000002 CerP … InCh… LVZNXIM… "CCCC… C26H54…      507. CerP          
#> 3 LipidBlast000003 CerP … InCh… KKMUWYA… "CCCC… C28H58…      535. CerP          
#> 4 LipidBlast000004 CerP … InCh… LYSHUFF… "CCCC… C30H62…      563. CerP          
#> 5 LipidBlast000005 CerP … InCh… OKWWFSI… "CCCC… C32H66…      591. CerP          
#> 6 LipidBlast000006 CerP … InCh… MKJOCAJ… "CCCC… C32H64…      589. CerP          
#> 7 LipidBlast000007 CerP … InCh… KZLFXFL… "CCCC… C34H70…      619. CerP          
#> 8 LipidBlast000008 CerP … InCh… GTSHVCJ… "CCCC… C36H74…      648. CerP          
#> # ℹ 7 more variables: ionization_mode <chr>, precursor_mz <dbl>,
#> #   precursor_type <chr>, retention_time <dbl>, ccs <dbl>, spectrum <chr>,
#> #   synonyms <list>