Comments (2)
Thank you, that's exactly what I was looking for :)
from rawrr.
Dear @YasinEl,
sure that is possible! Following what we have published yesterday :-) https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00866 you can even generate your own accessor function for peak noise values:
> rawfile <- file.path(Sys.getenv('HOME'), "Downloads", "20181113_010_autoQC01.raw")
> rawfile
[1] "/Users/tobiasko/Downloads/20181113_010_autoQC01.raw"
> i <- 9594
> S <- rawrr::readSpectrum(rawfile = rawfile, scan = i)
> S
[[1]]
Total Ion Current: 62374688
Scan Low Mass: 100
Scan High Mass: 1015
Scan Start Time (Min): 15.42
Scan Number: 9594
Base Peak Intensity: 12894520
Base Peak Mass: 860.4223
Scan Mode: FTMS + c NSI Full ms2 [email protected] [100.0000-1015.0000]
======= Instrument data ===== : NULL
Multiple Injection: h
Multi Inject Info: IT=2.8
AGC: On
Micro Scan Count: 1
Scan Segment: 1
Scan Event: 2
Master Index: 0
Charge State: 2
Monoisotopic M/Z: 0.0000
Ion Injection Time (ms): 2.811
Max. Ion Time (ms): 55.00
FT Resolution: 30000
MS2 Isolation Width: 1.40
MS2 Isolation Offset: 0.00
AGC Target: 100000
HCD Energy: 27.00
Analyzer Temperature: 30.29
=== Mass Calibration: NULL
Conversion Parameter B: 211689007.9670
Conversion Parameter C: -88620884.7343
Temperature Comp. (ppm): -6.03
RF Comp. (ppm): 0.00
Space Charge Comp. (ppm): -0.06
Resolution Comp. (ppm): -0.04
Number of Lock Masses: 2
Lock Mass #1 (m/z): 371.1010
Lock Mass #2 (m/z): 445.1200
Lock Mass #3 (m/z): 0.0000
LM Search Window (ppm): 15.0
LM Search Window (mmu): 0.0
Number of LM Found: 0
Last Locking (sec): 0.0
LM m/z-Correction (ppm): 3.15
=== Ion Optics Settings: NULL
S-Lens RF Level: 60.00
S-Lens Voltage (V): 21.00
Skimmer Voltage (V): 15.00
Inject Flatapole Offset (V): 5.00
Bent Flatapole DC (V): 2.00
MP2 and MP3 RF (V): 628.00
Gate Lens Voltage (V): 1.00
C-Trap RF (V): 1010.0
==== Diagnostic Data: NULL
Dynamic RT Shift (min): 0.00
Intens Comp Factor: 0.6852
Res. Dep. Intens: 1.333
CTCD NumF: 0
CTCD Comp: 5.321
CTCD ScScr: 0.000
RawOvFtT: 225788.1
LC FWHM parameter: 15.0
Rod: 0
PS Inj. Time (ms): 13.750
AGC PS Mode: -1
AGC PS Diag: 0
HCD Energy eV: 23.681
AGC Fill: 1.00
Injection t0: -0.020
t0 FLP: 860.42
Access Id: 0
Analog Input 1 (V): 0.000
Analog Input 2 (V): 0.000
attr(,"class")
[1] "rawrrSpectrumSet"
> S[[1]]$noises
[1] 24563.38 24559.59 25864.96 25866.78 25427.94 25113.02 24894.63 26068.89 26085.78 26253.31 26342.82 27035.06 27033.53
[14] 27020.81 26991.55 26970.78 26607.42 26574.18 26572.64 26468.55 26400.05 25540.01 26206.67 26684.34 26786.95 26877.38
[27] 26939.79 26968.94 26817.41 26723.80 26561.83 26464.12 26463.38 26447.87 26265.03 26261.98 26243.98 26241.00 26228.81
[40] 26250.30 26257.45 26278.55 26287.98 26357.33 26371.79 26379.98 26363.67 26358.24 26336.62 26298.83 26282.51 26277.18
[53] 26271.39 26238.96 26200.41 26197.32 26183.76 26183.35 26178.21 26106.25 26097.72 26089.20 26084.02 26083.65 26175.71
[66] 26197.22 26556.51 27122.80 27162.43 27282.32 27324.60 27639.10 27645.09 27693.55 27705.69 27748.30 27814.58 27996.20
[79] 28021.08 28033.02 28051.78 28057.82 28160.99 28136.65 28120.05 28082.64 27954.59 27945.63 27826.57 27809.94 27808.66
[92] 27790.52 27772.53 27498.53 27480.24 27354.27 27316.66 26752.06 26566.07 26551.98 26509.03 26314.59 26317.16 26327.46
[105] 26342.01 26342.86 26357.41 26358.26 26365.94 26467.42 26616.55 26620.82 26690.80 26695.06 26699.44 26769.32 26777.12
[118] 26959.56 27029.97 27041.84 27235.08 27246.98 27259.08 27452.10 27463.33 27464.19 27465.21 27632.84 27716.98 27728.90
[131] 27922.12 27934.00 27946.07 28069.81 28060.78 28051.75 27979.89 27970.97 27887.41
> makeAccessor(key = "noises", returnType = "double")
function(x) {
stopifnot(is.rawrrSpectrum(x))
if (key %in% names(x)) {
cl <- call(paste0("as.", returnType), x[[key]])
eval(cl)
} else {
stop(paste0(key, " is not available!"))
}
}
<bytecode: 0x7fb257d45248>
<environment: 0x7fb25b5476a8>
> noises <- makeAccessor(key = "noises", returnType = "double")
> noises(S[[1]])
[1] 24563.38 24559.59 25864.96 25866.78 25427.94 25113.02 24894.63 26068.89 26085.78 26253.31 26342.82 27035.06 27033.53
[14] 27020.81 26991.55 26970.78 26607.42 26574.18 26572.64 26468.55 26400.05 25540.01 26206.67 26684.34 26786.95 26877.38
[27] 26939.79 26968.94 26817.41 26723.80 26561.83 26464.12 26463.38 26447.87 26265.03 26261.98 26243.98 26241.00 26228.81
[40] 26250.30 26257.45 26278.55 26287.98 26357.33 26371.79 26379.98 26363.67 26358.24 26336.62 26298.83 26282.51 26277.18
[53] 26271.39 26238.96 26200.41 26197.32 26183.76 26183.35 26178.21 26106.25 26097.72 26089.20 26084.02 26083.65 26175.71
[66] 26197.22 26556.51 27122.80 27162.43 27282.32 27324.60 27639.10 27645.09 27693.55 27705.69 27748.30 27814.58 27996.20
[79] 28021.08 28033.02 28051.78 28057.82 28160.99 28136.65 28120.05 28082.64 27954.59 27945.63 27826.57 27809.94 27808.66
[92] 27790.52 27772.53 27498.53 27480.24 27354.27 27316.66 26752.06 26566.07 26551.98 26509.03 26314.59 26317.16 26327.46
[105] 26342.01 26342.86 26357.41 26358.26 26365.94 26467.42 26616.55 26620.82 26690.80 26695.06 26699.44 26769.32 26777.12
[118] 26959.56 27029.97 27041.84 27235.08 27246.98 27259.08 27452.10 27463.33 27464.19 27465.21 27632.84 27716.98 27728.90
[131] 27922.12 27934.00 27946.07 28069.81 28060.78 28051.75 27979.89 27970.97 27887.41
>
Hope this helps!
from rawrr.
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
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from rawrr.