findEIC {RMassBank} | R Documentation

## Extract EICs

### Description

Extract EICs from raw data for a determined mass window.

### Usage

    findEIC(
      msRaw,
      mz,
      limit = NULL,
      rtLimit = NA,
      headerCache = NULL,
      floatingRecalibration = NULL,
      peaksCache = NULL,
      polarity = NA,
      msLevel = 1,
      precursor = NULL
    )

### Arguments

`msRaw` | The mzR file handle
`mz` | The mass or mass range to extract the EIC for: either a single mass (with the range specified by `limit` below) or a mass range in the form of `c(min, max)`.
`limit` | If a single mass was given for `mz`: the mass window to extract. A limit of 0.001 means that the EIC will be returned for `[mz - 0.001, mz + 0.001]`.
`rtLimit` | If given, the retention time limits in form `c(rtmin, rtmax)` in seconds.
`headerCache` | If present, the complete `mzR::header(msRaw)`. Passing this value is useful if spectra for multiple compounds should be extracted from the same mzML file, since it avoids getting the data freshly from `msRaw` for every compound.
`floatingRecalibration` | A fitting function that `predict()`s a mass shift based on the retention time. Can be used if a lockmass calibration is known (however you have to build the calibration yourself.)
`peaksCache` | If present, the complete output of `mzR::peaks(msRaw)`. This speeds up the lookup if multiple compounds should be searched in the same file.

### Value

A `[rt, intensity, scan]` matrix (`scan` being the scan number.)

### Author(s)

Michael A. Stravs, Eawag <michael.stravs@eawag.ch>

### See Also

findMsMsHR

[Package RMassBank version 3.2.0 Index]