riMatrix {TargetSearch} | R Documentation

## Retention Time Index Matrix

### Description

A function to search for retention index RI markers.

### Usage

    riMatrix(samples, rim)

### Arguments

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

### 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 adjustment. See `fixRI`.

### Value

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

### Note

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`.

### 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) )

[Package TargetSearch version 1.48.0 Index]