peakFind {TargetSearch} | R Documentation

## Intensities and RI matrices

### Description

This function returns a list of the intensities and RI matrices that were searched.

### Usage

    peakFind(samples, Lib, cor_RI,
        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 with corrected RI values. See `medianRILib`.
`cor_RI` | A matrix of correlating selective masses RI for every sample. See `sampleRI`.
`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 `tsMSdata` object.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`ImportSamples`, `ImportLibrary`, `medianRILib`, `sampleRI`, `tsMSdata`, `tsLib`, `tsSample`

### Examples

    require(TargetSearchData)
    data(TSExample)

    # get RI file path
    RI.path <- file.path(find.package("TargetSearchData"), "gc-ms-data")
    refLibrary <- ImportLibrary(file.path(RI.path,"library.txt"))

    # update RI file path
    RIpath(sampleDescription) <- RI.path

    peakData <- peakFind(sampleDescription, refLibrary, corRI)
    # show peak Intensities.
    head(Intensity(peakData), 2)

    # How to get intensities for a particular metabolite
    # just select the identifier. Here extract the intensities
    # for the first metabolite in the library
    IntMatrix <- Intensity(peakData)[[1]]

[Package TargetSearch version 1.44.0 Index]