Retention Time Index Matrix

Description

A function to search for retention index RI markers.

Usage

riMatrix(samples, rim)

Arguments

Details

This function works similar to RIcorrect, but searches for RI markers in RI files (not in CDF files). Can be used to retrieve the retention times of RI markers in already processed files.

Note that it does not perform any RI adjusment. See fixRI.

Value

A retention time matrix of the found retention time markers. Every column represents a sample and rows RT markers.

Author(s)

Alvaro Cuadros-Inostroza

See Also

RIcorrect, FAMEoutliers,ImportSamples, ImportFameSettings, fixRI

Examples

require(TargetSearchData)
# import refLibrary, rimLimits and sampleDescription.
data(TSExample)
# get the CDF files
cdfpath <- file.path(find.package("TargetSearchData"), "gc-ms-data")

# select a subset of samples
smp <- sampleDescription[1:4]

# update the CDF path
CDFpath(smp) <- cdfpath

# make a copy of the RI markers object
rim <- rimLimits

# run RIcorrect
RImat <- RIcorrect(smp, rim, massRange = c(85,320), writeCDF4path=FALSE,
           Window = 15, pp.method = "ppc", IntThreshold = 50)

# extract the retention times of the markers
RImat2 <- riMatrix(smp, rim)

# both matrices should be equal
stopifnot( all.equal(RImat, RImat2, tolerance=1e-8) )