as.compoundData: Convert Data to compoundData Class

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

Convert Data to compoundData Class

Description

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.

Usage

as.compoundData(
  e_data,
  f_data,
  e_meta,
  edata_cname,
  fdata_cname,
  mass_cname,
  compound_cname,
  ...
)

Arguments

e_data	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.
f_data	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.
e_meta	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.
edata_cname	character string specifying the name of the column containing a unique identifier for each peak/mass in e_data and e_meta.
fdata_cname	character string specifying the name of the column containing the sample identifiers in f_data.
mass_cname	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.
compound_cname	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)

Details

as.compoundData constructs a compoundData object which is an ftmsData object where the rows of e_data correspond to compounds.

EMSL-Computing/fticRanalysis documentation built on Dec. 18, 2024, 9:51 p.m.