adjustRT: Peak alignment

In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description

adjustRT is a wrapper of the xcms::adjustRtime from xcms package. It performs the alignment of chromatographic peaks of samples. There are two methods that can be used depending on the parameters object.

Usage

adjustRT(...)

Arguments

...	Arguments passed on to xcms::adjustRtime

Details

A) peakGroups: Correction of RT based on alignment of features (grouped peaks) in most of samples. See xcms::adjustRtime-peakGroups for info.

B) obiwarp: Alignment based on the complete mz-rt data. This method does not require any identified peaks or defined features. See xcms::adjustRtime-obiwarp for info.

The parameter object xcms::ObiwarpParam or xcms::PeakGroupsParam created for including in the adjustRT function defines which method will be used.

Value

XCMSnExp object with peaks aligned. Note that adjustRT discard all previous peak grouping in the obtained object and thus, a new grouping process might be required. The xcms::ObiwarpParam function returns a ObiwarpParam class instance with all of the settings specified for obiwarp retention time adjustment and alignment.

Author(s)

Johannes Rainer

See Also

retcor for the old retention time correction methods. plotAdjustedRtime for visualization of alignment results.

Other retention time correction methods: adjustRtime-obiwarp, adjustRtime-peakGroups

sipss/AlpsLCMS documentation built on May 13, 2021, 6:18 p.m.