fcor-methods {msbase} | R Documentation

## Similarity measures for peak-list comparison

### Description

Computes the:

- dotprod
- covariance
- sum of agreing intensities of two Massvectors.

### 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 the non-crossing matching
`method` | type of dissimilarity: dotprod – dotproduct of matching intensities. cov – covariance of matching intensities. soai – sum of agrein intensities of matching intensities.
`norm` | how to scale the itensities vnorm – l=2 norm, vector length normalization. tic – l=1 norm, total ion count normalization. student – root mean square normalization (see. `scale`) zscore – z-score normalization. (see. `scale`)
`theta` | "numeric" how to weight the non-matching peaks.
`N` | default 0 - total length of alinged peak-lists.
`range` | experimental

### Value

The Dissimilarity.

### Methods

obx = "Massvector", oby = "Massvector"
  : returns similarity
obx = "Massvectorlist", oby = "Massvector"
  : returs numeric vector
obx = "Massvectorlist", oby = "NULL"
  : returns object of class `dist`

### Author(s)

Witold E. Wolski witek96@users.sourceforge.net http://r4proteomics.sourceforge.net

### See Also

`fdist`,`fbinary`

### Examples

    data(pldata)
    fcor(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="no",method="dotprod")
    fcor(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
    #search with one peak-list in a bunch of peak-lists
    fcor(pldata,pldata[[1]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
    #compute distance matrix of peak-lists and cluster
    tmp<-fcor(pldata,NULL,error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
    plot(hclust(tmp,method="average"))

[Package msbase version 1.1.1 Index]