medianRILib {TargetSearch} | R Documentation |
Return a tsLib
object with the median RI of the selective masses across samples.
medianRILib(samples, Lib, makeReport = FALSE, pdfFile = "medianLibRep.pdf", columns = c("SPECTRUM", "RETENTION_TIME_INDEX"), showProgressBar = FALSE)
samples |
A tsSample object created by ImportSamples function. |
Lib |
A tsLib object created by ImportLibrary function. |
makeReport |
Logical. If TRUE will report the RI deviations for every metabolite
in the library. |
pdfFile |
The file name where the report will be saved. |
columns |
A numeric vector with the positions of the columns 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 tsLib
object. It will update the slot med_RI
which contains
the median RI of every searched metabolite.
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
ImportSamples
, ImportLibrary
, tsLib-class
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 # update median RI refLibrary <- medianRILib(sampleDescription, refLibrary) # perhaps you need to adjust the library RI of one metabolite and the allowed time # deviation (first time deviation window) libRI(refLibrary)[5] <- 306500 RIdev(refLibrary)[5,1] <- 2000 refLibrary <- medianRILib(sampleDescription, refLibrary)