Description Usage Arguments Author(s)
View source: R/parameters_db.R
This function sets all the parameters used for downstream pre-processing of user's raw MS data based on specific LC-MS platform or parameters optimization. The database will be under an real-time update based on the progress in this field.
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 | SetPeakParam(
platform = "general",
Peak_method = "centWave",
RT_method = "loess",
mzdiff,
snthresh,
bw,
ppm,
min_peakwidth,
max_peakwidth,
noise,
prefilter,
value_of_prefilter,
fwhm,
steps,
sigma,
profStep,
minFraction,
minSamples,
maxFeatures,
max,
extra,
span,
smooth,
family,
fitgauss,
verbose.columns,
mzCenterFun,
integrate,
...
)
|
platform |
Character, specify the LC-MS platform used in pratice, including "UPLC-Q/E", "UPLC-Q/TOF","UPLC-T/TOF","UPLC-Ion_Trap","UPLC-Orbitrap","UPLC-G2S","HPLC-Q/TOF","HPLC-Ion_Trap","HPLC-Orbitrap","HPLC-S/Q". Default is "general", which is a more common option for all platform. If the platform is not listed above, please use this one. |
Peak_method |
Character, specify the algorithm to perform peak detection. "centwave" to use the CentWave algorithm, and "matchedFilter" to use the MatchedFilter algorithm. |
RT_method |
Character, specify the algorithm to perform tetention time alignment, including "loess" and "obiwarp". Default is "loess". |
mzdiff |
Numeric, specify the minimum m/z difference for signals to be considered as different features when retention times are overlapping. |
snthresh |
Numeric, specify the signal to noise threshold. |
bw |
Numeric, specify the band width (sd or half width at half maximum) of gaussian smoothing kernel to be applied during peak grouping. |
ppm |
Numeric, specify the mass error in ppm. |
min_peakwidth |
Numeric, specify the minimum peak width in seconds.Only work for 'centWave'. |
max_peakwidth |
Numeric, specify the maximum peak width in seconds.Only work for 'centWave'. |
noise |
Numeric, specify the noise level for peaking picking.Only work for 'centWave'. |
prefilter |
Numeric, specify the scan number threshold for prefilter.Only work for 'centWave'. |
value_of_prefilter |
Numeric, specify the scan abundance threshold for prefilter. Only work for 'centWave'. |
fwhm |
numeric specifying the full width at half maximum of matched filtration gaussian model peak. Only work for 'matchedFilter'. |
steps |
numeric defining the number of bins to be merged before filtration. Only work for 'matchedFilter'. |
sigma |
numeric specifying the standard deviation (width) of the matched filtration model peak. Only work for 'matchedFilter'. |
profStep |
numeric defining the bin size (in mz dimension) to be used for the profile matrix generation. Only work for 'obiwarp'. |
minFraction |
Numeric, specify fraction of samples in each group that contain the feature for it to be grouped. |
minSamples |
Numeric, specify minimum number of sample(s) in each group that contain the feature for it to be included. |
maxFeatures |
Numeric, specify the maximum number of features to be identified. |
... |
Other parameters, including max,extra,span,smooth,family,fitgauss, verbose.columns,mzCenterFun,integrate. Usually don't need to change. |
Zhiqiang Pang zhiqiang.pang@mail.mcgill.ca, Jasmine Chong jasmine.chong@mail.mcgill.ca, Mai Yamamoto yamamoto.mai@mail.mcgill.ca, and Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)
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