fbinary-methods {msbase}R Documentation

Binary measures for pairwise peak-list comparison

Description

Binary measures are comptued on entries of a contingency table.
Implements the:

Arguments

obx see below in Methods section
oby see above in Methods section
error measurement error
ppm if TRUE then error in parts per million(ppm), in arbitrary units otherwise.
weight should mass accuracy be weighted
uniq if TRUE compute non-crossing matching.
method type of dissimilarity:
  • rmi – relative mutual information
  • fm – fowlkes mallows statistics
  • hg – huberts gamma
  • gower – gower coefficient
N default 0 - total length of alinged peak-lists.
range experimental

Methods

obx = "numeric", oby = "numeric"
expects two numeric vectors as parameters, returns scalar
obx = "Massvector", oby = "Massvector"
returns scalar (numeric)
obx = "Massvectorlist", oby = "Massvector"
returns a vector with all pairwise dissimilaritities.
obx = "Massvectorlist", oby = "NULL"
returns object of class dist
obx = "list", oby = "NULL"
returns object of class dist

Author(s)

Witold E. Wolski witek96@users.sourceforge.net

Examples

# resolve multiple matches.
data(pldata)
pl1 <- pldata[[1]]
pl2 <- pldata[[2]]
fbinary(pl1,pl2,error=400,ppm=TRUE,theta=1,weight=FALSE,method="rmi",uniq=TRUE,N=0)
# dont resolve multiple matches.
fbinary(pl1,pl2,error=400,ppm=TRUE,theta=0.2,weight=FALSE,method="rmi",uniq=FALSE)
fbinary(pl1,pl2,error=400,ppm=TRUE,theta=0.2,weight=FALSE,method="hg")
fbinary(pl1,pl2,error=400,ppm=TRUE,theta=0.2,weight=TRUE,method="gower")
fbinary(pl1,pl2,error=400,ppm=TRUE,theta=0.2,weight=TRUE,method="fm")
# seach with one peak-list in a list of peak-lists.
fbinary(pldata,pl1,error=400,ppm=TRUE,theta=0.2,weight=TRUE,method="fm")
# compute distances (dissimilarities) and cluster.
tmp <- fbinary(pldata,NULL,error=400,ppm=TRUE,theta=0.2,weight=TRUE,method="fm")
plot(hclust(tmp,method="average"))

[Package msbase version 1.4.0 Index]