fbinary-methods {msbase} | R Documentation |
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
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 |
Massvector-class
Witold E. Wolski witek96@users.sourceforge.net http://r4proteomics.sourceforge.net
# 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"))