FEMsettings: Example settings for 'metaMS'
In metaMS: MS-based metabolomics annotation pipeline
Description
Usage
Format
Author(s)
See Also
Examples
Description
Examples of settings needed for functions runLC and
runGC: Synapt.RP, Synapt.NP, TSQXLS.GC and Orbitrap.RP. These four
particular settings are fine-tuned for the analysis of LC-MS runs,
both normal-phase and reverse-phase chromatography (Waters Synapt
G1-Thermo Orbitrap)and GC-MS experiments (ThermoXLS TQQ).
Usage
1
Format
Four objects of class metaMSsettings.
Author(s)
Ron Wehrens and Pietro Franceschi
See Also
Examples
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## 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,
Retcor = list(
method = "linear",
family = "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)
## For reverse-phase LC, settings are very similar: the only difference
## is in the alignment settings
Synapt.RP <- Synapt.NP
metaSetting(Synapt.RP, "protocolName") <- "Synapt.QTOF.RP"
metaSetting(Synapt.RP, "Alignment") <- list(
min.class.fraction = .3,
min.class.size = 3,
mzwid = 0.1,
bws = c(30, 10),
missingratio = 0.2,
extraratio = 0.1,
Retcor = list(
method = "linear",
family = "symmetric"),
fillPeaks = TRUE)
## For the orbitrap.RP
Orbitrap.RP <- metaMSsettings(protocolName = "Orbitrap",
chrom = "LC",
PeakPicking = list(
method = "centWave",
ppm = 5,
prefilter = c(3,10000),
peakwidth = c(15,40)),
Alignment = list(
bws = 30,
min.class.fraction = 0.3,
min.class.size = 3,
mzwid = 0.01,
Retcor = list(
method = "obiwarp",
profStep = 0.2),
fillPeaks = TRUE),
CAMERA = list(
perfwhm = 0.6,
cor_eic_th = 0.7,
ppm = 5))
metaSetting(Orbitrap.RP, "match2DB") <- list(
rtdiff = 1.5,
rtval = .1,
mzdiff = 0.005,
ppm = 5,
minfeat = 2)
metaSetting(Orbitrap.RP, "DBconstruction") <- list(
minfeat = 3,
rttol = .3,
mztol = .01)
## For the thermo TQ
TSQXLS.GC <- metaMSsettings("protocolName" = "TSQXLS.QQQ.GC",
"chrom" = "GC",
PeakPicking = list(
method = "matchedFilter",
step = 0.5,
steps = 2,
mzdiff = .5,
fwhm = 5,
snthresh = 2,
max = 500),
CAMERA = list(perfwhm = 1))
metaSetting(TSQXLS.GC, "DBconstruction") <- list(
minintens = 0.0,
rttol = .1,
intensityMeasure = "maxo",
DBthreshold = .80,
minfeat = 5)
metaSetting(TSQXLS.GC, "match2DB") <- list(
simthresh = 0.80,
timeComparison = "rt",
rtdiff = .5,
RIdiff = 5,
minfeat = 2)
metaSetting(TSQXLS.GC, "matchIrrelevants") <- list(
irrelevantClasses = c("Bleeding", "Plasticizers"),
timeComparison = "rt",
RIdiff = 2,
rtdiff = .05,
simthresh = 0.70)
metaSetting(TSQXLS.GC, "betweenSamples") <- list(
min.class.fraction = .5,
min.class.size = 5,
timeComparison = "rt",
rtdiff = .05,
RIdiff = 2,
simthresh = .95)
## End(Not run)
metaMS documentation built on Nov. 8, 2020, 8:21 p.m.
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Description Usage Format Author(s) See Also Examples
Description
Examples of settings needed for functions runLC and
runGC: Synapt.RP, Synapt.NP, TSQXLS.GC and Orbitrap.RP. These four
particular settings are fine-tuned for the analysis of LC-MS runs,
both normal-phase and reverse-phase chromatography (Waters Synapt
G1-Thermo Orbitrap)and GC-MS experiments (ThermoXLS TQQ).
Usage
1 |
Format
Four objects of class metaMSsettings.
Author(s)
Ron Wehrens and Pietro Franceschi
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 | ## 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,
Retcor = list(
method = "linear",
family = "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)
## For reverse-phase LC, settings are very similar: the only difference
## is in the alignment settings
Synapt.RP <- Synapt.NP
metaSetting(Synapt.RP, "protocolName") <- "Synapt.QTOF.RP"
metaSetting(Synapt.RP, "Alignment") <- list(
min.class.fraction = .3,
min.class.size = 3,
mzwid = 0.1,
bws = c(30, 10),
missingratio = 0.2,
extraratio = 0.1,
Retcor = list(
method = "linear",
family = "symmetric"),
fillPeaks = TRUE)
## For the orbitrap.RP
Orbitrap.RP <- metaMSsettings(protocolName = "Orbitrap",
chrom = "LC",
PeakPicking = list(
method = "centWave",
ppm = 5,
prefilter = c(3,10000),
peakwidth = c(15,40)),
Alignment = list(
bws = 30,
min.class.fraction = 0.3,
min.class.size = 3,
mzwid = 0.01,
Retcor = list(
method = "obiwarp",
profStep = 0.2),
fillPeaks = TRUE),
CAMERA = list(
perfwhm = 0.6,
cor_eic_th = 0.7,
ppm = 5))
metaSetting(Orbitrap.RP, "match2DB") <- list(
rtdiff = 1.5,
rtval = .1,
mzdiff = 0.005,
ppm = 5,
minfeat = 2)
metaSetting(Orbitrap.RP, "DBconstruction") <- list(
minfeat = 3,
rttol = .3,
mztol = .01)
## For the thermo TQ
TSQXLS.GC <- metaMSsettings("protocolName" = "TSQXLS.QQQ.GC",
"chrom" = "GC",
PeakPicking = list(
method = "matchedFilter",
step = 0.5,
steps = 2,
mzdiff = .5,
fwhm = 5,
snthresh = 2,
max = 500),
CAMERA = list(perfwhm = 1))
metaSetting(TSQXLS.GC, "DBconstruction") <- list(
minintens = 0.0,
rttol = .1,
intensityMeasure = "maxo",
DBthreshold = .80,
minfeat = 5)
metaSetting(TSQXLS.GC, "match2DB") <- list(
simthresh = 0.80,
timeComparison = "rt",
rtdiff = .5,
RIdiff = 5,
minfeat = 2)
metaSetting(TSQXLS.GC, "matchIrrelevants") <- list(
irrelevantClasses = c("Bleeding", "Plasticizers"),
timeComparison = "rt",
RIdiff = 2,
rtdiff = .05,
simthresh = 0.70)
metaSetting(TSQXLS.GC, "betweenSamples") <- list(
min.class.fraction = .5,
min.class.size = 5,
timeComparison = "rt",
rtdiff = .05,
RIdiff = 2,
simthresh = .95)
## End(Not run)
|
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