fbinary-methods {msbase}R Documentation

Methods for Function “fbinary” in Package 'msbase'

Description

Binary measures are comptued on entries of a contingency table.

Implements the:
Relative Mutual information,
Fowlkes Mallows statistics M_11/sqrt(M_1Y*M_1X),
the Gower coefficient (M_01^XY+M_10^XY)/(M_01^XY+M_10^XY+M_11^XY),
and Huberts Γ

Arguments

obx see above
oby see above
error measurement error
ppm if TRUE then error in parts per million, in arbitrary units otherwise
weight should mass accuracy be weighted
uniq if TRUE compute optimal aligmnent
method type of dissimilarity: c("rmi","fm","hg","gower")
range experimental

Methods

obx = "numeric", oby = "numeric"
expects two numeric vectors as parameters
obx = "Massvector", oby = "Massvector"
expects two massvectors as parameters Massvector-class
obx = "Massvectorlist", oby = "Massvector"
returns a vector with the all pairwise dissimilaritities between the entries in obx and the Massvector oby
obx = "Massvectorlist", oby = "NULL"
computes a dissimilarity matrix
obx = "list", oby = "NULL"
computes a dissimilarity matrix

Author(s)

Witold E. Wolski witek96@users.sourceforge.net http://r4proteomics.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)
# 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 1.0.0 Index]