ROCDATA {msbase} | R Documentation

## Transformation and other factors of the pairwise peak-lists Comparsion Process

### Description

Scores of the binary and intensity based measures for PMF and MS/MS datasets. The file contains the sensitivity and specificity PAUC obtained for each set of factors. In addition it contains the AUC and max(sum(specificity+sensitivity)). For an analysis of variance, to determine the best performing measures see the Sweave file varan.Rnw in the doc directory of the package.

### Usage

    data(pmf.binary); data(pmf.intensity);data(msms.binary);data(msms.intensity)

### Format

A dataframe with 10 columns and 96 (Binary) or rows.

### Details

Column names and they content.

- ABBREV – abreviation of CP
- Measure – Measure (dissimilarity measure)
  - Binary – measures.
    - fm – Fowlkes Mallows
    - hg – Huberts Gamma
    - rmi – relative mutual information
    - gower – gower coefficient
  - Intensity – based measures.
    - cov – Covariance
    - soai – sum of agreeing intensities
    - euclidean – euclidean distance
    - manhattan – Manhattan distance
    - canberra – Canberra distance
    - simindex – similarity index
    - dotprod – dot product measure
- Trans (intensity transformation)
  - N – raw data
  - S – square root transformation
  - L – log transformation
  - R – ranks of intensities
- Scale – scaling of peak intensities
  - T – total ion count scaling
  - N – vector length
  - S – root mean square
  - Z – z-score
- theta – weigth of non-matching peaks
  - 0.5
  - 1
  - 2
- Weight – weighting of measurement accuracy
  - M – without non-crossing matching
  - W – with non-crossing matching
- Noncross (non-crossing matching)
  - A – the non-crossing matching was determined
  - O – the non-crossing matching was not determined
- Length – length of aligned PLs
  - N=0
  - N=250 (PMF) ; N=800 (MSMS)
- AUC – Area under the reveiver operator characteristic curve.
- MaxSSp – Maxiumum of sensitivity + specificity on the ROC curve.
- FPPAUC – specificity PAUC.
- TPPAUC – sensitivity PAUC

### Source

http://r4proteomics.sourceforge.net

### References

Wolski et al. "Transformation and other factors of the MS peak-list comparsion process"(2005)

### Examples

    data(pmf.binary)
    data(pmf.intensity)
    data(msms.binary)
    data(msms.intensity)

[Package msbase version 1.1.1 Index]