Description Usage Arguments Details Value Author(s) References See Also
This method tries to remove saturation effects from the intensity counts.
1 2 3 4  ## S4 method for signature 'MSnSet'
requantify(object, saturationThreshold,
method=c("sum", "reference", "th.mean", "th.median",
"th.weighted.mean"), ...)

object 
An 
saturationThreshold 

method 

... 
further arguments passed to internal functions. Currently

Currently requantify
supports 3 (5) different requantification
methods.
"sum"
is the simplest requantification method. All ions of a
peptide below the saturation threshold are summed to get the new intensity.
This method accept an additional argument, namely onlyCommonIsotopes
If onlyCommonIsotopes=TRUE
(default) all ions that are not seen in
all runs are removed and only the common seen ions are summed. In contrast
onlyCommonIsotopes=FALSE
sums all ions regardless they are present
in all runs.
In "reference"
the run that has the most unsaturated ions in common
with all the other runs. If there are more than one run, the most intense is
used as reference. The other runs are corrected as
follows:
Find common ions between current and the reference run.
Divide the intensities of the common ions and calculate the mean of these quotients as a run specific scaling factor.
Multiply the unsaturated ions of the current run by the scaling factor and replace the saturated ones by the product of the scaling factor and the intensities of their corresponding ions in the reference run.
Sum the rescaled ion intensities.
The "th.*"
methods are nearly identical. All of them calculate the
theoretical isotopic distribution for the given sequence of the peptide.
Subsequently the unsaturated ions are divided by their theoretical
proportion and the mean
/median
/weighted.mean
(proportions are used as weights) of these intensities are calculated per
charge state. The sum of the charge state values is used as requantified
intensity for this peptide.
If requantifyAll=FALSE
(default) just peptides with at least one
saturated ion are requantified (unsaturated peptides are unaffected). If
requantify=TRUE
all peptides even these where all ions are below
saturationThreshold
are requantified by their theoretical
distribution.
MSnSet
where the
assayData
are requantified.
Sebastian Gibb mail@sebastiangibb.de and Pavel Shliaha
See discussion on github: https://github.com/lgatto/synapter/issues/39
MSnSet documentation: MSnSet
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