TSExample {TargetSearch} | R Documentation |
A TargetSearch
example GC-MS data. This datasets contains TargetSearch object
examples generated from a E.coli salt stress experiment (See package TargetSearchData).
data(TSExample)
The data contains the following objects:
a tsSample
object. The sample description.
a tsLib
object. The reference library.
a tsRim
object. The RI markers definition.
a matrix object. The retention time of the RI markers.
a matrix object. The sample RI.
a tsMSdata
object. The intensities and RIs of all the
masses that were searched for.
a tsProfile
object. The metabolite profile.
This dataset contain only the objects. The actual source files are provided by the package TargetSearchData.
ImportLibrary
,
ImportSamples
,
ImportFameSettings
,
# 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)