retentionCorr {adductomicsR} | R Documentation

## loess-based retention time deviation correction

### Description

loess-based retention time deviation correction

### Usage

    retentionCorr(adductSpectra = NULL,
    smoothingSpan = NULL, nMissing = 1,
    nExtra = 1, folds = 7, outputFileDir = NULL)

### Arguments

`adductSpectra` | AdductSpec object
`smoothingSpan` | numeric. fixed smoothing span, argument to loess. If argument is not supplied then optimal smoothing span is calculated for each file seperately.
`nMissing` | numeric. maximum number of missing files for a MS/MS scan group to be utilized in the loess retention time deviation model. Roughly 15 percent missing values is a good starting point (e.g. nMissing=10 for 68 samples).
`nExtra` | numeric maximum number of extra scans above the total number of files for a MS/MS scan group to be utilized in the loess retention time deviation model. If a MS/MS scan group consists of many scans far in excess of the number of files then potentially MS/MS scans from large tailing peaks or isobars may be erroneously grouped together and used to adjust retention time incorrectly.
`folds` | numeric. number of cross validation steps to perform in identifying optimal smoothing span parameter (see: bisoreg package for more details)
`outputFileDir` | character full path to a directory to save the output images

### Value

LOESS RT models as adductSpectra AdductSpec object

[Package adductomicsR version 1.6.0 Index]