combineMS2.removeContam: remove any possible contaminants identified as repeating...

In WMBEdmands/CompMS2miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

remove any possible contaminants identified as repeating sequences of isobaric ions of high spectral similarity.

Usage

combineMS2.removeContam(object, ...)

Arguments

object	a "compMS2" class object.
ms1Abs	numeric ms1 mass to charge absolute error for hierarchical clustering of MS1 masses (default = 0.01). Utilizes the median method of the hclust function of the fastcluster package.
maxRtGap	numeric maximum retention time gap (in seconds) between two isobaric ions. Sequences of possible contaminants will be identified using this difference in retention time (default = 60).
nContams	numeric number of isobaric ions in a sequence separated by a maximum retention time gap (maxRtGap). Any sequences of isobaric ions greater than or equal to this number will be removed (default = 10).
minSimScore	numeric minimum spectral similarity score (values between 0-1). If any isobar in a sequence of possible contaminants is below this minimum mean dot product similarity score then it will not be removed. This is to ensure that only true isobaric contaminants are removed and spectra which have been grouped amongst them are not erroneously removed (default = 0.8).
remContam	logical should possible contaminant spectra be automatically removed from the object (default = TRUE), If FALSE the contaminant plot will still be printed but the spectra will not be removed. In this way the user can interactively determine suitable parameters prior to spectrum removal.

Details

The function produces plots to visualize the contaminants identified. If you suspect all isobaric ions across the gradient are contaminants then you can set the argument maxRtGap to Infinite (maxRtGap=Inf). N.B. Any spectrum which is not sufficiently similar (specSimScore) to the rest of the potential contaminants across the gradient will not be erroneously removed.

Value

a "compMS2" class object with the composite spectra and all metID information of any contaminants identified removed. Any correlation or spectral similarity networks will also have to be recalculated.

Examples

compMS2contamRem <- combineMS2(compMS2Example, 'removeContam', maxRtGap=Inf, 
                               nContams=4)

WMBEdmands/CompMS2miner documentation built on May 9, 2019, 10:02 p.m.