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]