xcms

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Regarding the steps of operating FillChromPeaksParam

3

The following are the steps I took to analyze GC-MS. When it comes to FillChromPeaksParam, this function requires the use of **`XCMSnExp`** objects. The objects I use in the fifth...

v-v1150n

Import methods

5

Here are the implementation of the generics function `loadResults()` and its respective method for the parameters RDataParam and PlainTextParam. I still have bugs in order to build examples/unit test with...

philouail

Add a function to coerce between xcms result objects. This is related to https://github.com/krispir/cpc/issues/5

jorainer

For gap filling with `fillChromPeaks()` on MS2 chrom peaks we have to make sure we're filling in data from MS2 spectra of the correct isolation window too. The `chromatograms,XcmsExperiment` does...

jorainer

Duplicate values created by fillChromPeaks

1

Our workflow is findChromPeaks, groupChromPeaks and fillChromPeaks. I am finding duplicate values in the output from fillChromPeaks - I have attached a sample file. Is this expected behaviour where peaks...

frankyWk

Retention time alignment using a combination of LamaParama and subset-based alignment

2

Hello, We are trying to explore how to improve the processing speed for the retention time alignment step, which often takes 2-5x longer than the peak detection. One option we...

CLUES-Emory

adjustRtime not conducted with large dataset, but working after register(SerialParam())

6

With a large dataset of >500 injections (Orbitrap Q-Exactive, full scan, not centroided), I encountered that the retention time adjustment did not execute. The script kept running, so that later...

c-ze

Using xcms and Spectra package

3

Dear all, From what I understand, the connection between xcms and Spectra is made with MsExperiment objects. I'm trying to reproduce the xcmsTutorials but with fictitious data in Spectra, but...

felipe-mansoldo

xcms on conda

7

i am trying to setup on an HPC system using conda. I have tried R 4.4.1, as well as R 4.3.1, and in each case i cannot seem to get...

cbroeckl

Add chromPeakSummary function and a fix

3

This PR adds the `chromPeakSummary()` method and a first implementation to calculate the peak shape quality from @wkumler on chrom peak results (thanks to @pablovgd for contributing). In addition, it...

jorainer