wsiFilter.massvector {mscalib}R Documentation

Smilanski Filtering

Description

The function returns the inidces of masses identified as chemical noise.

Usage

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

Arguments

... further arguments.
fraction maximal fraction (nr masses in branch)/(length of massvector) of branche to be prune.
mdist minimal distance to branch to be prune. The unit of this distance are Daltons.
object massvector.

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

indices Indices of masses which are identified as being nonpeptide.

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

wsFilter.massvector, wsdist.massvector, wsFilter.massvectorlist,

Examples

 data(mv1)
 data(mv2)
 length(mv1)
 length(wsFilter(mv1))
 length(mv2)
 length(wsFilter(mv2))

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