medianRILib {TargetSearch} | R Documentation

## 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.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`ImportSamples`, `ImportLibrary`, `tsLib-class`

### Examples

    require(TargetSearchData)
    data(TSExample)

    # 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)

[Package TargetSearch version 1.42.1 Index]