medianRILib {TargetSearch}R Documentation

Median RI library correction

Description

Return a tsLib object with the median RI of the selective masses across samples.

Usage

medianRILib(samples, Lib, makeReport = FALSE, pdfFile = "medianLibRep.pdf",
        columns = c("SPECTRUM", "RETENTION_TIME_INDEX"), showProgressBar = FALSE)

Arguments

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?

Value

A tsLib object. It will update the slot med_RI which contains the median RI of every searched metabolite.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

ImportSamples, ImportLibrary, tsLib-class

Examples

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)


[Package TargetSearch version 1.0.0 Index]