peakFind {TargetSearch} | R Documentation |
This function returns a list of the intensities and RI matrices that were searched.
peakFind(samples, Lib, cor_RI, columns = c("SPECTRUM", "RETENTION_TIME_INDEX"), showProgressBar = FALSE)
samples |
A tsSample object created by ImportSamples function. |
Lib |
A tsLib object created by ImportLibrary function with
corrected RI values. See medianRILib . |
cor_RI |
A matrix of correlating selective masses RI for every sample.
See sampleRI . |
columns |
A numeric vector with the column positions of SPECTRUM and
RETENTION_TIME_INDEX or a character vector with the header names of those
columns. |
showProgressBar |
Logical. Should the progress bar be displayed? |
A tsMSdata
object.
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
ImportSamples
, ImportLibrary
, medianRILib
,
sampleRI
, tsMSdata
, tsLib
,
tsSample
require(TargetSearchData) data(TargetSearchData) # get RI file path RI.path <- file.path(.find.package("TargetSearchData"), "gc-ms-data") # update RI file path RIpath(sampleDescription) <- RI.path peakData <- peakFind(sampleDescription, refLibrary, corRI) # show peak Intensities. head(Intensity(peakData)) # How to get intensities for a particular metabolite # # make a library index using top masses libId <- libId(refLibrary, sel = FALSE) # get the peak intensities of Metabolite 1, for example, of every mass int.1 <- Intensity(peakData)[libId == 1,] # this assigns the mass values to the row names of int.1 rownames(int.1) <- topMass(refLibrary)[[1]]