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LCMS table

Source: R/cd_source_class.R
cd_source.Rd

An LCMS table extends annotation_table() to represent annotation data for an LCMS experiment. Columns representing m/z and retention time are required for an lcms_table.

Usage

cd_source(
  source,
  sheets = c(1, 1),
  tag = "CD",
  mz_column = "mz",
  rt_column = "rt",
  id_column = "id",
  data = NULL,
  ...
)

Arguments

source

(character) The path to the Compound Discoverer Excel files to import. Both the compounds and isomers file should be included, in that order.

sheets

(character, numeric, integer) The name or index of the sheets to read from the source file(s). A sheet should be provided for each input file. The default is c(1, 1).

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 "CD".

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 cd_source object. This object has no output slots.

Inheritance

A cd_source object inherits the following struct classes:

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

See also

Other annotation sources: annotation_database, annotation_table, ls_source, mspurity_source

Other annotation tables: annotation_table, ls_source

Examples

M <- cd_source(
        sheets = c(2, 2),
        mz_column = "mz",
        rt_column = "rt",
        id_column = "id",
        tag = character(0),
        data = data.frame(),
        source = character(0))