TargetSearchData {TargetSearchData} | R Documentation

## Example GC-MS data for TargetSearch Package

### Description

A `TargetSearch` example GC-MS data. This package contains raw NetCDF files from a E.coli salt stress experiment, extracted peak list of each NetCDF file and three tab-delimted text files: a sample description, a reference library and a retention index marker definition. The data is a subset of the original data from 200-400 seconds and 85-320 m/z.

### Usage

            data(TargetSearchData)

### Format

The data contains the following objects:

sampleDescription
  a `tsSample` object. The sample description.
refLibrary
  a `tsLib` object. The reference library.
rimLimits
  a `tsRim` object. The RI markers definition.
RImatrix
  a matrix object. The retention time of the RI markers.
corRI
  a matrix object. The sample RI.
peakData
  a `tsMSdata` object. The intensities and RIs of all the masses that were searched for.
metabProfile
  a `tsProfile` object. The metabolite profile.

### Details

All files are located in `gc-ms-data` subdirectory.

### See Also

`ImportLibrary`, `ImportSamples`, `ImportFameSettings`,

### Examples

    require(TargetSearch)

    ## The directory with the NetCDF GC-MS files
    cdfpath <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
    cdfpath
    list.files(cdfpath)
    samp.file <- file.path(cdfpath, "samples.txt")
    rim.file  <- file.path(cdfpath, "rimLimits.txt")
    lib.file  <- file.path(cdfpath, "library.txt")

    # import files from package
    sampleDescription <- ImportSamples(samp.file, CDFpath = cdfpath, RIpath = ".")
    refLibrary        <- ImportLibrary(lib.file)
    rimLimits         <- ImportFameSettings(rim.file, mass = 87)
    # perform RI correction
    RImatrix          <- RIcorrect(sampleDescription, rimLimits, massRange = c(85,320),
                       IntThreshold = 25, pp.method = "ppc", Window = 15)
    # update median RI
    refLibrary        <- medianRILib(sampleDescription, refLibrary)
    # get the sample RI
    corRI             <- sampleRI(sampleDescription, refLibrary, r_thres = 0.95)
    # obtain the peak Intensities of all the masses in the library
    peakData          <- peakFind(sampleDescription, refLibrary, corRI)
    # make a profile of the metabolite data
    metabProfile      <- Profile(sampleDescription, refLibrary, peakData, r_thres = 0.95)

    # show the metabolite profile
    profileInfo(metabProfile)
    # show the matrix intensities
    Intensity(metabProfile)

[Package TargetSearchData version 1.0.0 Index]