wsFilter.massvector {mscalib}R Documentation

Smilanski Filtering

Description

Removes chemical noise from the massvectorlist.

Usage

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

Arguments

... further parameters.
fraction maximal size of branche (nr masses in branch)/(length of massvector) to be cut.
mdist minimal distance of branch to be cut.
object massvector.
peptides 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

massvector returns either a massvector of nonpeptide masses or massvector of peptide masses.

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.massvectorlist,

Examples

 data(mv1)
 tmp <- wsFilter(mv1,peptide=FALSE)
 plot(tmp)
 tmp <- wsFilter(mv1,peptide=TRUE)
 plot(tmp)

[Package mscalib version 0.5.9 Index]