readChromatogram(...)

[cpanse]

refactor rawDiag::readXICs(rawfile, masses=unique(RAW$PrecursorMass), tol=1000)

returns a nested S3 list

[[22]]
$mass
[1] 554.2606

$times
[1] 0.1216408 0.1516450 0.4810452 0.5409557 0.7801059

$intensities
[1] 3005.061 4328.104 3658.515 3862.011 4992.357

$filename
[1] "sample.raw"

attr(,"class")
[1] "list" "XIC" 

attr(,"class")
[1] "list" "XICs"
> X[[20]]
$mass
[1] 653.3617

$times
 [1] 0.001619751 0.031642766 0.061663615 0.091651065 0.121640750 0.151644970
 [7] 0.181667770 0.211526280 0.241284530 0.271307600 0.301222200 0.331145000
[13] 0.361147270 0.391168050 0.421057700 0.450970250 0.481045180 0.510989030
[19] 0.540955750 0.570893130 0.600724580 0.630620300 0.660428770 0.690318400
[25] 0.720320350 0.750197620 0.780105920

$intensities
 [1] 374171.6 405717.2 350914.7 373948.4 328768.2 425965.4 360327.9 453483.1
 [9] 445894.1 430538.9 422901.3 545305.5 433117.8 357588.1 435593.4 351018.2
[17] 407768.5 406468.8 446027.8 385148.5 579871.8 461409.0 390769.3 458988.6
[25] 378339.6 480078.4 467780.0

$filename
[1] "sample.raw"

attr(,"class")

with additional attributes:

input:

• scan filter
• type : XIC, BPC, TIC

type BPC, TIC need no additional parameters. XIC requires mz and tolerance in addition.

output:

• type, e.g, XIC, TIC, BPC (base peak chromatogram)
• tolerance (in ppm)
• mz
• scan filter

[tobiasko]

Our old readXIC method did not support Chromatograms for UV, PDA, and Analog detectors (other detectors than MS). Is that correct @cpanse? Due to requests like fgcz/rawDiag#61 we should think about supporting this in the future.

[tobiasko]

This would mean that the detector becomes an additional attribute of the function.

[cpanse]

at least we should have that in mind to add this functionality later. C

…

On Fri, Aug 28, 2020 at 2:35 PM Tobias Kockmann ***@***.***> wrote: This would mean that the detector becomes an additional attribute of the function. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFMYYZV3FIRG2DWGHZB6KDSC6QB5ANCNFSM4QKMPDBA> .

[tobiasko]

@cpanse How would I instruct readChromatogram to return a TIC or BPC instead of an XIC?

[cpanse]

cp@lilith:~/__checkouts/R/rawR  (master)> mono exec/rawR.exe ~/Downloads/20181113_010_autoQC01.raw chromatogram ms2|cat -n|head
     1	# TIC chromatogram (20886 points)
     2	# Base Peak chromatogram (20886 points)
     3	# MassRange chromatogram (20886 points)
     4	rt,intensity.BasePeak,intensity.TIC,intensity.MassRange
     5	0.007,2958,22506,18929
     6	0.008,2935,27142,23437
     7	0.010,11758,62303,58274
     8	0.011,3062,50225,43532
     9	0.013,3045,44352,38631
    10	0.014,3134,45077,40341