metaSetting-methods: Get or set values in metaMSsettings objects

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

Get or set values in metaMSsettings objects

Description

Accessor function for metaMSsettings objects, allowing to get or set values from individual slots.

Methods

signature(object = "metaMSsettings")

Get or set values from individual slots in a metaMSsettings objects.

See Also

FEMsettings

Examples

## Not run: 
## The three sets of settings are created as follows:
Synapt.NP <- metaMSsettings(protocolName = "Synapt.QTOF.NP",
                            chrom = "LC",
                            PeakPicking = list(
                              method = "matchedFilter",
                              step = 0.05,
                              fwhm = 20,
                              snthresh = 4,
                              max = 50),
                            Alignment = list(
                              min.class.fraction = .3,
                              min.class.size = 3,
                              mzwid = 0.1,
                              bws = c(130, 10),
                              missingratio = 0.2,
                              extraratio = 0.1,
                              retcormethod = "linear",
                              retcorfamily = "symmetric",            
                              fillPeaks = TRUE),
                            CAMERA = list(
                              perfwhm = 0.6,
                              cor_eic_th = 0.7,
                              ppm= 5))
metaSetting(Synapt.NP, "match2DB") <- list(
            rtdiff = 1.5,
            rtval = .1,
            mzdiff = 0.005,
            ppm = 5,
            minfeat = 2)
metaSetting(Synapt.NP, "DBconstruction") <- list(
            minfeat = 3,
            rttol = .3,
            mztol = .01)

## End(Not run)

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.