TSExample {TargetSearch} | R Documentation

## Example GC-MS data for TargetSearch Package

### Description

A `TargetSearch` example GC-MS data. This datasets contains TargetSearch object examples generated from a E.coli salt stress experiment (See package TargetSearchData).

### Usage

        data(TSExample)

### 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

This dataset contain only the objects. The actual source files are provided by the package TargetSearchData.

### See Also

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

### Examples

    # this run an example pipeline
    require(TargetSearchData)

    ## 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)

    # update NCDF4
    sampleDescription <- ncdf4Convert(sampleDescription, path=".")

    # 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 TargetSearch version 1.43.3 Index]