Converts a list object or several data.frames of FT-MS data to an object of the class 'compoundData'. Objects of the class 'compoundData' are lists with three obligatory components e_data, f_data, and e_meta.
as.compoundData(
e_data,
f_data,
e_meta,
edata_cname,
fdata_cname,
mass_cname,
compound_cname,
...
)a \(p \times n + 1\) data.frame of expression data, where \(p\) is the number of observed compounds and \(n\) is the number of samples. Each row corresponds to data for each peak. One column specifying a unique identifier for each peak/mass (row) must be present.
a data.frame with \(n\) rows. Each row corresponds to a sample with one column giving the unique sample identifiers found in e_data column names and other columns providing qualitative and/or quantitative traits of each sample.
a data.frame with \(p\) rows. Each row corresponds to a compound with one column giving a unique peak/identifier (must be named the same as the column in e_data) and other columns giving meta information. At a minimum a column giving the mass of each peak and a column giving molecular formulae or columns giving elemental counts must be present.
character string specifying the name of the column containing a unique identifier for each peak/mass in e_data and e_meta.
character string specifying the name of the column containing the sample identifiers in f_data.
character string specifying the name of the column containing the peak/mass identifiers in e_meta. Note: this is often the same as edata_cname for cases where mass is used as a unique identifier.
character string specifying the name of the column containing the compound identifier in e_meta. This is a compound identifier related to a database (e.g. MetaCyc)
further arguments (see as.peakData)
as.compoundData constructs a compoundData object which is an ftmsData object where the rows of e_data correspond to compounds.