fcor-methods {msbase}R Documentation

Methods for Function “fcor” in Package 'msbase'

Description

Methods for function fcor in package .GlobalEnv

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 optimal aligmnent
method type of dissimilarity: c("dotprod","soai")
norm how to scale the itensities c("student","zscore","tic","no")
theta "numeric" how to weight the non-matching peaks.
range experimental

Value

The Dissimilarity.

Methods

obx = "Massvector", oby = "Massvector"
:
obx = "Massvectorlist", oby = "Massvector"
:
obx = "Massvectorlist", oby = "NULL"
:

Author(s)

Witold E. Wolski witek96@users.sourceforge.net http://r4proteomics.sourceforge.net

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 1.0.0 Index]