FindPeaks {TargetSearch} | R Documentation

## Extract peaks from chromatogram files

### Description

This function extracts the maximum intensity of a list of masses in a given RI window.

### Usage

    FindPeaks(my.files, refLib,
        columns = c("SPECTRUM", "RETENTION_TIME_INDEX", "RETENTION_TIME"),
        showProgressBar = FALSE)

### Arguments

`my.files` | A character vector naming RI files to be searched.
`refLib` | A numeric matrix with three columns or a list of three column matrices. The second column contains the masses and the first and third column contains the RI limits.
`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?

### Details

The reference library parameter `refLib` can be either a single three-column matrix or a list of such matrices. If it is a list, the length must match the length of `my.files`. In this case, every component will be used to iteratively search in the corresponding file.

The RI files format can be either "text" or "binary". The type is detected dinamically.

### Value

A `tsMSdata` object.

### Note

This is an internal function not intended to be invoked directly.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`medianRILib`, `sampleRI`, `peakFind`, `tsMSdata`

### Examples

    # load example CDF files
    require(TargetSearchData)
    # load pre-calculated example data and objects
    data(TSExample)

    # get RI file path
    RI.path <- file.path(find.package("TargetSearchData"), "gc-ms-data")
    # update RI file path
    RIpath(sampleDescription) <- RI.path

    my.files <- RIfiles(sampleDescription)
    # make a three column matrix: lower RI, mass, upper RI
    refLib   <- refLib(refLibrary)
    head(refLib)

    # extract the peaks
    peaks <- FindPeaks(my.files, refLib)

[Package TargetSearch version 1.40.3 Index]