retentionCorr: loess-based retention time deviation correction
In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

loess-based retention time deviation correction

1
2
3

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

`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