retentionCorr: loess-based retention time deviation correction

Description Usage Arguments Value

Description

loess-based retention time deviation correction

Usage

1
2
3
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


JosieLHayes/adductomicsR documentation built on May 5, 2019, 9:43 p.m.