MAIT (version 1.6.0)

Biotransformations: Biotransformations of the significant data contained in a MAIT object are identified.

Description

This function takes a MAIT-class object having significant features already detected and looks up for biotransformations between them. MAIT has a default biotransformation table that will be used if no other table is specified via the bioTable input parameter.

Usage

Biotransformations(MAIT.object = NULL,  peakPrecision = 0.005, bioTable = NULL,  adductTable = NULL, adductAnnotation = FALSE)

Arguments

MAIT.object

A MAIT-class object where significant features have already been found.

peakPrecision

Maximum difference between the peak masses differences and the values shown in bioTable to be considered as a biotransformation. As default the value is 0.005 Da.

bioTable

Table containing the biotransformations to be looked for in the signData input. By default it is taken the MAIT-class biotransformations table.

adductTable

Table containing the adducts to be looked for in the signData input. By default it is taken the MAIT-class positive adducts table. If this argument is set to "negAdducts", then the default table for negative adducts is taken instead. It is possible to use a user-defined adduct table

adductAnnotation

If it is set to TRUE, both adduct and Biotransformations annotation stages are performed.

Value

A MAIT-class object with the updated biotransformations slot

See Also

spectralAnova spectralTStudent

Examples

data(MAIT_sample)
MAIT<-spectralSigFeatures(MAIT,p.adj="fdr",parametric=TRUE)
MAIT<-Biotransformations(MAIT.object = MAIT, peakPrecision = 0.005)
MAIT@FeatureInfo@biotransformations; #Detected Biotransformations