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msPurity source

Source: R/mspurity_source_class.R
mspurity_source.Rd

An annotation source for importing an annotation table from the format created by the msPurity package.

Usage

mspurity_source(
  source,
  tag = "msPurity",
  mz_column = "mz",
  rt_column = "rt",
  id_column = "id",
  data = NULL,
  ...
)

Arguments

source

(ANY) The source of annotation data.

tag

(character) A (short) character string that is used to represent this source e.g. in column names or source columns when used in a workflow. The default is "msPurity".

mz_column

(character) The column name of the annotation data.frame containing m/z values. The default is "mz".

rt_column

(character) The column name of the annotation data.frame containing retention time values. The default is "rt".

id_column

(character) The column name of the annotation data.frame containing row identifers. If NULL This will be generated automatically. The default is "id".

data

(data.frame, NULL) A data.frame of annotation data. The default is NULL.

...

Additional slots and values passed to struct_class.

Value

A mspurity_source object. This object has no output slots.

Details

This object makes use of functionality from the following packages:

  • msPurity

Inheritance

A mspurity_source object inherits the following struct classes:

[mspurity_source] -> [lcms_table] -> [annotation_table] -> [annotation_source] -> [struct_class]

References

Lawson, Nigel T, Weber, M. RJ, Jones, R. M, Chetwynd, J. A, Blanco R, Alejandro G, Guida D, Riccardo, Viant, R. M, Dunn, B W (2017). "msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics." Analytical Chemistry, 89, 2432-2439. doi:10.1021/acs.analchem.6b04358 https://doi.org/10.1021/acs.analchem.6b04358.

See also

Other annotation sources: annotation_database(), annotation_table(), cd_source(), ls_source(), mwb_study_source()

Other annotation tables: annotation_table(), cd_source(), ls_source()

Examples

M <- mspurity_source(
        mz_column = "mz",
        rt_column = "rt",
        id_column = "id",
        tag = character(0),
        data = data.frame(),
        source = "ANY")