getEICs fix#31
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getEICs() failing when multiple EICs extracted from 2 or more files as these are out of order compared to the pspectra index. To fix, a template xeic@eic list created and then filled out of order as necessary by lapply(). xraw scantimes also updated from parent xcmsSet object, and other cosmetic changes to cat() outputs
to reflect that an xcmsRaw() object is not input
getAllPeakEICs assumes each scan has the same RT accross all samples. Fixed by approximating the scans to the rt range for the sample with the longest rt range
sneumann
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Mar 21, 2020
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sneumann
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Hi, any chance we can have a unit test checking for the changes ?
Can you have a look at the failing travis ? Anything I'd need to do on our side ?
| peaks <- CAMERA:::getPeaks(object@xcmsSet, smpls[a]) | ||
| eic <- lapply (pspecS, function(pc) { | ||
| invisible(lapply (pspecS, function(pc) { | ||
| cnt <<- cnt + 1 |
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<<- immediately jumps at me. Any chance to avoid that ?
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Not sure why this would be an issue, becuase as I understand it <<- applies to the parent environment, which in this case is PlotEICs() where cnt is assigned at line 17 (and so not to the the global environment)?
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incorporates all changes to date |
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