riMatrix: Retention Time Index Matrix
In TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Description Usage Arguments Details Value Note Author(s) See Also Examples

A function to search for retention index RI markers.

1	riMatrix(samples, rim)

`samples`	A `tsSample` object created by `ImportSamples` function.
`rim`	A `tsRim` object. See `ImportFameSettings`.

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 adjustment. See fixRI.

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

In case the RI files are in text format and their column names are not standard (for example, when the files were generated with another software), use the global option 'TS_RI_columns' or transform the RI files to TargetSearch binary format. See the documentation in function text2bin.

Alvaro Cuadros-Inostroza

RIcorrect, FAMEoutliers,ImportSamples, ImportFameSettings, fixRI

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) )