getrecalib.massvectorlist {mscalib}R Documentation

Precalibration

Description

Obtain the error model using the wavelength analysis of the peaklist.

Usage

## S3 method for class 'massvectorlist':
getrecalib(object,plot=FALSE,...)

Arguments

... further parameters.
object massvectorlist
plot logical; TRUE - A graphic showing the F(omega). default FALSE

Details

Precalibration method utilizes the knowledge that masses of peptides are in equidistant spaced clusters. The wavelength of the massesvector can be determined as described by Wool. The comparision of the experimental wavelength with the theoretical one, makes possible to find an affine function that corrects the masses. Chemical noise in the spectra may hamper the determination of mass list frequency. The package provides a function to filter chemical noise.

Value

caliblist caliblist with objects of class calibrestat.

Author(s)

Witold Wolski wolski@molgen.mpg.de

References

-
Wool A, Smilansky Z 2002. Precalibration of matrix-assisted laser desorption/ionization-time of flight spectra for peptide mass fingerprinting. Proteomics. 2(10):1365-73.
-
Wolski http://www.molgen.mpg.de/~wolski/mscalib

See Also

getrecalib.massvector, applyrecalib.massvector, massvector, calibrestat, wsFilter.massvectorlist,

Examples

 data(mvl)
 mvl<-mvl[1:100]
 res <- getrecalib(mvl)
 print(res)
 summary(res)
 image(res,what="Coef.Intercept")
 image(res,what="Coef.Slope")
 plot(res)
 hist(res)
 dres<-as.data.frame(res)
 plot(dres$Coef.Intercept,dres$PQM,xlab="Coef.Intercept",ylab="PQM")
 #create subset.
 res2<-subset(res,PQM>10)
 length(res2)
 plot(res2)
 test<-applyrecalib(mvl, res2)
 plot(test)

[Package mscalib version 0.5.9 Index]