wsFilter.massvectorlist {mscalib}R Documentation

Smilanski Filtering

Description

Removes chemical noise from massvectors in the massvectorlist (if peptides argument TRUE) or returns it.

Usage

## S3 method for class 'massvectorlist':
wsFilter(object,mdist=0.25,fraction=0.2, peptides=TRUE,... )

Arguments

... further parameters.
fraction Maximal fraction (nr masses in branch)/(length of massvector) of branche to be prune.
mdist Minimal distance to branch to prune. The unit of the distance is Dalton.
object massvectorlist.
peptides logical; TRUE - returns peptides, FALSE - returns chemical noise.

Details

Chemical noise can be removed from the peptide mass lists due to the strong clustering of mono-isotopic peptide peaks. Following the distance measure and filtering method proposed by Wool Smilanski we developed an algorithm to classify masses as peptide and non-peptide. The algorithm is based on a modified distance measure and hierarchical clustering of all intra massvector distances.

Value

massvectorlist Returns a massvectorlist where the massvectors either contain the peptides or the non-peptides.

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.

See Also

wsiFilter.massvector, wsFilter.massvector,

Examples

 data(mvl)
 res <- wsFilter(mvl,peptides = TRUE)
 plot(res)
 res2 <- wsFilter(mvl,peptides = FALSE)
 plot(res2,col=2,add=TRUE)
 image(res2,what="lengthmv")
 hist(res)
 hist(res2,col=2,add=TRUE)

[Package mscalib version 0.5.9 Index]