getEIC-methods {xcms} | R Documentation

## Get extracted ion chromatograms for specified m/z ranges

### Description

Generate multiple extracted ion chromatograms for m/z values of interest. For `xcmsSet` objects, reread original raw data and apply precomputed retention time correction, if applicable.

Note that this method will always return profile, not raw data (with profile data being the binned data along M/Z). See details for further information.

### Arguments

`object` | the `xcmsRaw` or `xcmsSet` object
`mzrange` | Either a two column matrix with minimum or maximum m/z or a matrix of any dimensions containing columns `mzmin` and `mzmax`. If not specified, the method for `xcmsRaw` returns the base peak chromatogram (BPC, i.e. the most intense signal for each RT across all m/z). For `xcmsSet` objects the group data will be used if `mzrange` is not provided.
`rtrange` | A two column matrix the same size as `mzrange` with minimum and maximum retention times between which to return EIC data points. If not specified, the method returns the chromatogram for the full RT range. For `xcmsSet` objects, it may also be a single number specifying the time window around the peak to return EIC data points
`step` | step (bin) size to use for profile generation. Note that a value of `step = 0` is not supported.
`groupidx` | either character vector with names or integer vector with indicies of peak groups for which to get EICs
`sampleidx` | either character vector with names or integer vector with indicies of samples for which to get EICs
`rt` | `"corrected"` for using corrected retention times, or `"raw"` for using raw retention times

### Details

In contrast to the `rawEIC` method, that extracts the actual raw values, this method extracts them from the object's profile matrix (or if the provided `step` argument does not match the `profStep` of the `object` the profile matrix is calculated on the fly and the values returned).

### Value

For `xcmsSet` and `xcmsRaw` objects, an `xcmsEIC` object.

### Methods

object = "xcmsRaw"

  `getEIC(object, mzrange, rtrange = NULL, step = 0.1)`

object = "xcmsSet"

  `getEIC(object, mzrange, rtrange = 200, groupidx, sampleidx = sampnames(object), rt = c("corrected", "raw"))`

### See Also

`xcmsRaw-class`, `xcmsSet-class`, `xcmsEIC-class`, `rawEIC`

[Package xcms version 3.16.1 Index]