TSExample: Example GC-MS data for TargetSearch Package

In acinostroza/TargetSearch: A package for the analysis of GC-MS metabolite profiling data

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 <- tsd_data_path()
cdfpath
list.files(cdfpath)
# get files from TargetSearchData
samp.file <- tsd_file_path("samples.txt")
rim.file  <- tsd_file_path("rimLimits.txt")
lib.file  <- tsd_file_path("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)

acinostroza/TargetSearch documentation built on Nov. 22, 2024, 3:31 p.m.