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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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negative subsetting removes chromPeaks #707

Closed philouail closed 5 months ago

philouail commented 6 months ago

As the title says, negative subsetting seems to remove the chromPeaks detection even though the default for subsetting is supposed to keep the chromPeaks. 

> test <- loadXcmsData() 
> chromPeaks(test) 
+     head()          
 mz mzmin mzmax       rt    rtmin    rtmax     into     intb  maxo sn sample 
CP0001 594.0 594.0 594.0 2606.910 2586.566 2643.014 161042.2 146073.3  7850 11      1 
CP0002 577.0 577.0 577.0 2610.040 2586.566 2632.005 136105.2 128067.9  6215 11      1 
CP0003 307.0 307.0 307.0 2624.135 2597.520 2650.875 284782.4 264907.0 16872 20      1
CP0004 302.0 302.0 302.0 2622.560 2600.650 2646.158 687146.6 669778.1 30552 43      1 
CP0005 370.1 370.1 370.1 2679.209 2649.303 2706.052 449284.6 417225.3 25672 17      1
CP0006 427.0 427.0 427.0 2680.787 2649.303 2690.263 283334.7 263943.2 11025 13      1 

> test <- test[-1] 
> chromPeaks(test) 
+     head()     
mz mzmin mzmax rt rtmin rtmax into intb maxo sn sample