readStdInfo {metaMS} | R Documentation

## 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.

### 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
    }

[Package metaMS version 1.20.0 Index]