medianRILib: Median RI library correction

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

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 = NULL, 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	Either NULL, a character vector, or an integer vector. In most cases, leave it as NULL. This parameter is used to configure the column names or positions of RI text files. See the documentation on the text2bin function for further details.
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(TSExample)

# get RI file path
RI.path <- file.path(find.package("TargetSearchData"), "gc-ms-data")
# update RI file path
RIpath(sampleDescription) <- RI.path
# Import Library
refLibrary        <- ImportLibrary(file.path(RI.path,'library.txt'))
# 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)

TargetSearch documentation built on March 12, 2021, 2 a.m.