TargetSearch (version 1.28.1)

medianRILib: 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", "RETENTION_TIME"), 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, RETENTION_TIME_INDEX, and RETENTION_TIME 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.

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
# 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)