Comments (10)
Perfect, it works!
also @tobiasko I think personally it would be useful to restrict an XIC by retention time, but it would be useful to have the option for both if not too difficult.
Thanks again,
Tara
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Hi Tara,
thanks for your positive feedback and for asking these questions! 😀
Regarding the restriction of extraction: I think the API, or more precisely the GetChromatogramData
method, see allows you to define a startScan
and endScan
argument to restrict the import. But currently, we call the method using -1
and -1
see
which most likely means without restriction. I think this could be changed, but would require some code changes on the C# level and we would need to think about how to pass these arguments from the R layer to C# and incorporate the arguments as attributes to the chromatogram object.
But in essence, it would be a very useful extension. Not sure why we didn't do it right away. 😜
In terms of functionality, what would be your favourite option? Would you like to restrict by scan index, or by RT?
I would need to confirm all of the above with @cpanse first and have a look at the API docu.
Best,
Tobi
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@tobiasko https://github.com/fgcz/rawR/blob/44d3cc08b15ea66241647d3c1df47a3649cab682/src/rawR.cs#L769
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Aha. @cpanse, so does this mean the API explicitly returns zeros, but our code "discards" them? They are not written to the tmp file?
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Aha. @cpanse, so does this mean the API explicitly returns zeros, but our code "discards" them? They are not written to the temp file?
yes; for exactly that reason @TaraBartolec mentioned "it will likely increase the object size.'' For the moment we should deliver the libraries' output and we have to think about a slim
or trim
argument for removing the (0, 0) tuples.!?
from rawrr.
makes sense. or we think about a smarter way of storing the data inside the S3 object. If these vectors tend to be very sparse...well, use a sparse vector instead of a dense one. This will only store none zero values and plot()
will behave as expected.
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Dear @TaraBartolec @tobiasko
I uncommented line 769. can you have a look?
install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawR_0.1.2.tar.gz', repo=NULL)
C
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Hi Tara,
one last question since you tried to plot using the gglot library: How important is this to you? Our approach was to use base R for plotting to keep it simple from a developers perspective (no dependency, always available). But maybe this is not the most important aspect...
Greetings,
Tobi
from rawrr.
Hi Tobi,
It is not that important to use ggplot, I just used it as I wanted to restrain the retention times plotted and had trouble doing that with the plot() function for some reason. Being able to easily filter RT is the most important thing for the plotting for us.
Best,
Tara
from rawrr.
Ok, great! THX again for your feedback.
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Related Issues (20)
- Get information on gradient HOT 1
- Enhancement - Complete readIndex() function HOT 9
- Peak charges for MS1 spectras HOT 4
- Spectrum scan centroid mZ, intensity and noises values do not match HOT 2
- Error in Example: Length of "x" and "y" are not matching HOT 3
- Read noise value for profile mode mass spectra HOT 4
- Read_Spectrum - Sum Spectra
- unit should be minute / auc computation in seconds HOT 24
- validate_rawrrSpectrum 'StartTime' HOT 4
- "Error: line 1 did not have 9 elements" for readIndex() and readChromatogram() + "Error : No scan vector is provided"for readSpectrum HOT 9
- Problem executing readChromatogram inside Singularity container HOT 5
- Add a check if `input` file exists and is not empty
- Error in if (rvs != "No RAW file specified!") { : the condition has length > 1 HOT 16
- Switch to RawFileReader 5.0.93 HOT 2
- different total number of Spectra in msconvert, compomics/ThermoRawFileParser and thermofisherlsms/RawFileReader HOT 2
- Request for auc.rawrrChromatogram HOT 3
- profile mode in readSpectrum HOT 11
- speed up readIndex/readSpectrum by base::textConnection HOT 14
- rawrr::buildRawrrExe() fails HOT 6
- auc.rawrrChromatogram question
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