readStdInfo: Read information of GC injections of standards from a csv...

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

Read information of GC injections of standards from a csv file

Description

The csv contains all information necessary to process a series of injections of standards (GC-MS). Required fields: Name, RTman, monoMW, stdFile, and an identifier such as CAS or ChemspiderID. At the moment, the system is completely based on CAS, although this may change in the future.

Usage

readStdInfo(stdInfo, InputDir, sep = "", dec = ".", ...)

Arguments

stdInfo	Input file in csv format, containing information on standards.
InputDir	Location of input files.
sep, dec, ...	optional arguments to read.table.

Details

In addition to reading all information on the chemical standards (whcih will eventually be transferred into an in-house database), the function checks whether some input files are unavailable, and whether some data files are not used. In the first case, an error is returned, in the second case a warning.

Value

A data.frame

Author(s)

Ron Wehrens

Examples

if (require(metaMSdata)) {
  ## this will lead to the completed version of the R object that is also
  ## available by typing "data(threeStdsInfo)", now containing the
  ## directory information that is not available in the RData object.

  input.file <- list.files(system.file("extdata", package = "metaMSdata"),
                           pattern = "csv", full.names = TRUE)
  threeStdsInfo <- readStdInfo(input.file,
                               system.file("extdata", package = "metaMSdata"),
                               sep = ";", dec = ",")
  ## only one of the files is used to set up the database, the others
  ## are for testing annotation
}

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.