riMatrix {TargetSearch} | R Documentation |
A function to search for retention index RI markers.
riMatrix(samples, rim)
samples |
A |
rim |
A |
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) )