fcor-methods {msbase}R Documentation

Similarity measures for peak-list comparison

Description

Computes the:

Arguments

obx see above
oby see above
error measurement error
ppm if TRUE then error in parts per million, in arbitrary units otherwise
full if TRUE then compute for matching and not matching peaks
weight if TRUE weight differences between matching peaks.
uniq if TRUE compute the non-crossing matching
method type of dissimilarity:
  • dotprod – dotproduct of matching intensities.
  • cov – covariance of matching intensities.
  • soai – sum of agrein intensities of matching intensities.
norm how to scale the itensities
  • vnorm – l=2 norm, vector length normalization.
  • tic – l=1 norm, total ion count normalization.
  • student – root mean square normalization (see. scale)
  • zscore – z-score normalization. (see. scale)
theta "numeric" how to weight the non-matching peaks.
N default 0 - total length of alinged peak-lists.
range experimental

Value

The Dissimilarity.

Methods

obx = "Massvector", oby = "Massvector"
: returns similarity
obx = "Massvectorlist", oby = "Massvector"
: returs numeric vector
obx = "Massvectorlist", oby = "NULL"
: returns object of class dist

Author(s)

Witold E. Wolski witek96@users.sourceforge.net

See Also

fdist,fbinary

Examples

data(pldata)
fcor(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="no",method="dotprod")
fcor(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
#search with one peak-list in a bunch of peak-lists
fcor(pldata,pldata[[1]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
#compute distance matrix of peak-lists and cluster
tmp<-fcor(pldata,NULL,error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
plot(hclust(tmp,method="average"))

[Package msbase version 1.4.0 Index]