search

rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
Other
34 stars 20 forks source link

Meaningful colnames for calcPPS() result #4

Closed sneumann closed 9 years ago

sneumann commented 9 years ago

Currently, calcPPS() returns:

> calcPPS(iporesult$best_settings$xset)
     [,1] [,2] [,3] [,4]    [,5]
[1,]    0  692  462  194 81.4632

There should be reasonable column names mentioning 

 1. Space for experimentid of the Design of Experiments (0 since not known in calcPPS)
 2. Number of peaks
 3. Number of peaks without LIP and RP
 4. Reliable peaks (RP)
 5. Peak picking score (PPS)

Another question is why that is a one-row array, are there cases imaginable where calcPPS() returns multiple values ? If not, I suggest simplifying to a vector.

glibiseller commented 9 years ago

Thanks for your suggestions. In the next update I'll change the type of the return value of calcPPS() to a vector and add names.