fdist-methods {msbase}R Documentation

Methods for Function “fdist” in Package 'msbase'

Description

Computes euclidean or manhattan distance for two aligned vectors.

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("euclidean","manhattan")
norm how to scale the itensities c("student","zscore","tic","no")
theta "numeric" how to weight the non-matching peaks.
range experimental

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)
fdist(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="zscore",method="euclidean")
fdist(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="no",method="manhattan")
tmp <- fdist(pldata,NULL,error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="euclidean")
plot(hclust(tmp,method="average"))

[Package msbase version 1.0.0 Index]