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
- 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
References
Wolski et al. "Transformation and other factors of the
peptide MS peak-list comparsion process"(2005) See doc directory of
this package
Examples
data(pmf.binary)
data(pmf.intensity)
data(msms.binary)
data(msms.intensity)
[Package
msbase version 1.4.0
Index]