getEICs fix #31
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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
requested changes
Mar 21, 2020
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| pspecS <- pspec[which(object@psSamples[pspec] == smpls[a])] | ||
| ## getting ALL peaks from the current sample (not that bad) | ||
| 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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