as.CoreMSData: Create CoreMSData Object
In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

as.CoreMSData

R Documentation

Create CoreMSData Object

Description

Converts 'CoreMSrbind' object to 'CoreMSData' object

Usage

as.CoreMSData(
  all_data,
  index_cname = "Index",
  obs_mass_cname = "m/z",
  calib_mass_cname = "Calibrated m/z",
  calc_mass_cname = "Calculated m/z",
  pheight_cname = "Peak Height",
  error_cname = "Mass Error (ppm)",
  conf_cname = "Confidence Score",
  heteroatom_cname = "Heteroatom Class",
  iontype_cname = "Ion Type",
  file_cname = "Filename",
  monoiso_index_cname = "Mono Isotopic Index",
  mf_cname = "Molecular Formula",
  iso_cols = c("13C", "18O", "15N", "34S")
)

Arguments

`all_data`	a data.frame/CoreMSData object, should be the output of `read_CoreMS_data`
`index_cname`	a character string specifying the name of the column containing the index value
`obs_mass_cname`	a character string specifying the name of the column containing the observed mass to charge ratio (m/z) in `all_data`
`calib_mass_cname`	a character string specifying the name of the column containing the calibrated mass to charge ratio (m/z) in `all_data`
`calc_mass_cname`	a character string specifying the name of the column containing the calculated mass to charge ratio (m/z) in `all_data`
`pheight_cname`	a character string specifying the name of the column containing the peak height in `all_data`
`error_cname`	a character string specifying the name of the column containing the mass error (ppm) in `all_data`
`conf_cname`	a character string specifying the name of the column containing the confidence score in `all_data`
`heteroatom_cname`	a character string specifying the name of the column containing the heteroatom class in `all_data`
`iontype_cname`	a characer string specifying the name of the column containing the ion type in `all_data`
`file_cname`	a character string specifying the name of the column containing the filenames in `all_data`
`monoiso_index_cname`	a character string specifying the name of the column containing the monoisotopic index in `all_data`
`mf_cname`	a character string specifying the name of the column containing the molecular formula in `all_data`
`iso_cols`	a character vector specifying columns indicating the presence of isotopic peaks, e.g. a column "13C" with T/F specifying the presence of 13C. Defaults to `c("13C", "18O", "15N", "34S")`.