convert2MSP: Convert deconvoluted matrix into 'MSP'-object

In PlantDefenseMetabolism/MetabolomicTools: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Description

Convert deconvoluted matrix into MSP-object

Usage

convert2MSP(mm, splitPattern = "_", splitIndMZ = 1, splitIndRT = NULL, 
 rt = FALSE, names = FALSE, information = FALSE, classes = FALSE, adduct = FALSE)

Arguments

mm	matrix, mm has to have three columns with colnames "mz", "intensity" and "id" (order is not important). The column comprises information about the precursor ion which will be assessed by splitPattern and splitInd. Optionally, mm can have colnames "rt", "names", "information", "classes" and "adduct".
splitPattern	character, splitPattern is the pattern which separates elements and precursor m/z
splitIndMZ	numeric, the position of the precursor m/z in the character string concerning separation by splitPattern
splitIndRT	numeric or NULL, the position of the retention time in the character string concerning separation by splitPattern, if NULL the retention time will be the mean of all retention time values of the MS/MS feature fragments
rt	logical, should retention times be retrieved? If set to TRUE, convert2MSP will access the column "rt" in mm which contains the retention time values for each fragment when splitIndRT is NULL, if rt is set to TRUE and splitIndRT is numeric, convert2MSP will access the column "id" to get the retention time at position splitIndRT when splitting with splitPattern
names	logical, should names be retrieved? If set to TRUE, convert2MSP will access the column "names" in mm which contains the names of the metabolites
information	logical, should further information of metabolites be retrieved? If set to TRUE, convert2MSP will access the column "information" in mm which contains information about the metabolites
classes	logical, should classes of metabolites be retrieved? If set to TRUE, convert2MSP will access the column "classes" in mm which contains the names of the metabolites
adduct	logical, should adduct ion names of metabolites be retrieved? If set to TRUE, convert2MSP will access the column "adduct" in mm which contains the adduct ion names of the metabolites

Details

The function convert2MSP creates a data entry for each precursor ion. Each entry in the return object has the following information: Num Peaks and a list of fragments together with their intensities; it will further contain information on m/z values of the precursor ion, the retention time, metabolite names, classes, adduct ion name and further information. convert2MSP will access the columns "rt", "names", "information", "classes" and "adduct", respectively, if arguments are set to TRUE. The column "id" has to contain a unique identifier for each MS/MS feature. It is obligatory that each element in the column "id" contains the precursor m/z value, but may contain furhter elements (e.g. peak correlation value or retention time of the precursor ion). Information about the m/z value will be assessed by splitPattern and splitInd. E.g. items in the column "id" can be in the form of "1_163.23", which has to be accessed by setting splitPattern = "_" and splitInd = 2 to access the m/z value of the precursor ion (here: 162.23). If rt is set to TRUE and splitIndRT is NULL, convert2MSP will access the column "rt" to get the retention time values corresponding to each fragment and calculate the mean value, if rt is set to TRUE and splitIndRT numeric, convert2MSP will retrieve the retention time value from column "id".

Value

convert2MSP returns an object of class MSP

Author(s)

Thomas Naake, [e-mail]

Examples

data("sd02_deconvoluted", package = "MetCirc")
convert2MSP(mm = sd02_deconvoluted, splitPattern = " _ ", splitIndMZ = 2, 
 splitIndRT = NULL, rt = FALSE, names = FALSE, information = FALSE, 
 classes = FALSE, adduct = FALSE)

PlantDefenseMetabolism/MetabolomicTools documentation built on May 8, 2019, 2:53 p.m.