8 Calling MALDIquant from Clojure
A guide to using ClojisR to call R’s MALDIquant package from Clojure. This is useful for accessing MALDIquant features not yet in Ripple (peak alignment, spectrum averaging, feature matrices) and for cross-checking results against the reference implementation.
This is a companion to the NeuroKit2 comparison notebook, which demonstrates the same pattern using libpython-clj for Python interop.
Requires: R with MALDIquant installed (install.packages("MALDIquant") or ./setup_r.sh).
(ns ripple-book.maldiquant-interop
(:require
;; Table processing (https://scicloj.github.io/tablecloth/):
[tablecloth.api :as tc]
;; Interactive plotting via Plotly (https://scicloj.github.io/tableplot/):
[scicloj.tableplot.v1.plotly :as plotly]
;; R interop (https://github.com/scicloj/clojisr):
[clojisr.v1.r :as r :refer [r r->clj clj->r]]
;; Annotating kinds of visualizations (https://scicloj.github.io/kindly-noted/):
[scicloj.kindly.v4.kind :as kind]))Setup
ClojisR starts an R session automatically on first use. We just need to load the MALDIquant package.
(r "library(MALDIquant)")[1] "MALDIquant" "Rserve" "stats" "graphics" "grDevices"
[6] "utils" "datasets" "methods" "base"
ClojisR Basics
ClojisR provides three core functions for R interop:
| Function | Purpose |
|---|---|
(r ...) |
Evaluate an R expression (string or quoted form) |
(r->clj x) |
Convert an R object to Clojure data |
(clj->r x) |
Convert Clojure data to an R object |
Quoted forms use backtick syntax. Clojure values are spliced in with tilde (~).
Evaluating R expressions
As a string:
(r "1 + 1")[1] 2
As a quoted form (preferred — enables splicing Clojure values):
(r `(+ 1 1))[1] 2
Converting R results to Clojure
(r->clj (r `(seq 1 5)))[1 2 3 4 5]Splicing Clojure values into R
Use tilde (~) to inject Clojure values into quoted R expressions:
(def my-data [10.0 20.0 30.0 40.0 50.0])(r->clj (r `(mean ~my-data)))[30.0]Vectors, doubles, and strings all splice naturally. For keyword arguments in R functions, use Clojure keyword syntax:
(r->clj (r `(paste "hello" "world" :sep "-")))["hello-world"]Working with MALDIquant Objects
MALDIquant’s core data type is MassSpectrum — an S4 object with mass and intensity slots. We create one from Clojure vectors.
(def masses [100.0 200.0 300.0 400.0 500.0 600.0 700.0 800.0 900.0])(def intensities [0.1 0.3 0.8 1.5 0.9 0.2 0.4 1.2 0.6])Create a MassSpectrum object in R:
(r `(<- spec (createMassSpectrum :mass ~masses :intensity ~intensities)))S4 class type : MassSpectrum
Number of m/z values : 9
Range of m/z values : 100 - 900
Range of intensity values: 1e-01 - 1.5e+00
Memory usage : 1.227 KiB
Extract data back to Clojure:
(def r-masses (r->clj (r `(mass spec))))(def r-intensities (r->clj (r `(intensity spec))))(= (mapv double masses) r-masses)trueSingle-Spectrum Preprocessing
MALDIquant ships with fiedler2009subset — 16 real MALDI-TOF mass spectra from a pancreatic cancer study (Fiedler et al. 2009). We use the first spectrum to demonstrate each preprocessing step.
(r "data('fiedler2009subset', package='MALDIquant')")[1] "fiedler2009subset"
(def n-spectra (first (r->clj (r "length(fiedler2009subset)"))))n-spectra16(def n-points (first (r->clj (r "length(fiedler2009subset[[1]])"))))n-points42388Raw spectrum
(let [masses (r->clj (r "mass(fiedler2009subset[[1]])"))
intensities (r->clj (r "intensity(fiedler2009subset[[1]])"))
step 10
idx (range 0 (count masses) step)]
(-> (tc/dataset {:mass (mapv #(nth masses %) idx)
:intensity (mapv #(nth intensities %) idx)})
(plotly/base {:=width 800 :=height 300 :=x :mass :=y :intensity
:=x-title "m/z (Da)" :=y-title "Intensity"
:=title "Raw spectrum (fiedler2009subset #1)"})
(plotly/layer-line {:=mark-opacity 0.7})
plotly/plot))The raw spectrum shows a large baseline hump (chemical matrix signal) in the low-mass region, with analyte peaks sitting on top.
Trim to analysis range
(r "spec1 <- trim(fiedler2009subset[[1]], range=c(2000, 10000))")S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 5 - 27518
Memory usage : 411.156 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
Variance stabilization — transformIntensity
(r "spec1 <- transformIntensity(spec1, method='sqrt')")S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 2.236e+00 - 1.659e+02
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
Smoothing — smoothIntensity
(r "spec1 <- smoothIntensity(spec1, method='SavitzkyGolay', halfWindowSize=10)")S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 2.91e+00 - 1.656e+02
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
Baseline removal — removeBaseline
(r "spec1 <- removeBaseline(spec1, method='SNIP', iterations=25)")S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 1.044e+02
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
Normalization — calibrateIntensity
(r "spec1 <- calibrateIntensity(spec1, method='TIC')")S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 7.579e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
Verify TIC area is 1.0 (trapezoid rule):
(def real-area
(first (r->clj (r "m <- mass(spec1)
i <- intensity(spec1)
sum(diff(m) * (i[-1] + i[-length(i)]) / 2)"))))real-area1.0Peak detection — detectPeaks
(r "peaks1 <- detectPeaks(spec1, halfWindowSize=20, SNR=2, method='MAD')")S4 class type : MassPeaks
Number of m/z values : 252
Range of m/z values : 2012.127 - 9952.986
Range of intensity values: 9.657e-05 - 7.579e-03
Range of snr values : 2.003 - 157.225
Memory usage : 15.523 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
(def n-real-peaks (first (r->clj (r "length(peaks1)"))))n-real-peaks252Visualizing the result
(let [spec-m (r->clj (r "mass(spec1)"))
spec-i (r->clj (r "intensity(spec1)"))
peak-m (r->clj (r "mass(peaks1)"))
peak-i (r->clj (r "intensity(peaks1)"))
step 5
idx (range 0 (count spec-m) step)
sub-m (mapv #(nth spec-m %) idx)
sub-i (mapv #(nth spec-i %) idx)
ns (count sub-m)
np (count peak-m)]
(-> (tc/dataset {:mass (vec (concat sub-m peak-m))
:intensity (vec (concat sub-i peak-i))
:series (vec (concat (repeat ns "spectrum")
(repeat np "peaks")))})
(plotly/base {:=width 800 :=height 400 :=x :mass :=y :intensity :=color :series
:=x-title "m/z (Da)" :=y-title "Normalized intensity"
:=title "Preprocessed spectrum with detected peaks"})
(plotly/layer-line {:=mark-opacity 0.4})
(plotly/layer-point {:=mark-size 4 :=mark-opacity 0.8})
plotly/plot))Multi-Sample Workflow
So far we have processed a single spectrum. In a real experiment you have many spectra from different samples. MALDIquant provides batch functions that operate on lists of spectra — this is the workflow described in Gibb & Strimmer (2016), Sections 11.3.3–11.3.7.
Step 1: Batch preprocessing
All single-spectrum functions accept a list of spectra:
(r "spectra <- fiedler2009subset
spectra <- trim(spectra, range=c(2000, 10000))
spectra <- transformIntensity(spectra, method='sqrt')
spectra <- smoothIntensity(spectra, method='SavitzkyGolay', halfWindowSize=10)
spectra <- removeBaseline(spectra, method='SNIP', iterations=25)
spectra <- calibrateIntensity(spectra, method='TIC')")[[1]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 7.579e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
[[2]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 7.353e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M20
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid
[[3]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.992e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_H7.O14
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid
[[4]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.641e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_H7.P13
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid
[[5]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.213e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F10.L19
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid
[[6]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.144e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F10.L20
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid
[[7]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 5.975e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F9.L17
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid
[[8]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.002e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F9.L18
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid
[[9]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.703e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A6.A11
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid
[[10]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 6.895e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A6.A12
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid
[[11]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 5.557e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A8.A15
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid
[[12]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 5.85e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A8.A16
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid
[[13]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 4.145e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_C4.F7
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid
[[14]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 4.126e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_C4.F8
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid
[[15]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 4.285e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_D9.G17
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid
[[16]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.137 - 9999.734
Range of intensity values: 0e+00 - 4.019e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_D9.G18
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid
(def n-preprocessed (first (r->clj (r "length(spectra)"))))n-preprocessed16Step 2: Peak detection on all spectra
(r "all_peaks <- detectPeaks(spectra, halfWindowSize=20, SNR=2, method='MAD')")[[1]]
S4 class type : MassPeaks
Number of m/z values : 252
Range of m/z values : 2012.127 - 9952.986
Range of intensity values: 9.657e-05 - 7.579e-03
Range of snr values : 2.003 - 157.225
Memory usage : 15.523 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
[[2]]
S4 class type : MassPeaks
Number of m/z values : 243
Range of m/z values : 2002.301 - 9860.139
Range of intensity values: 9.209e-05 - 7.353e-03
Range of snr values : 2.012 - 160.65
Memory usage : 15.312 KiB
Name : Pankreas_HB_L_061019_G10.M20
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid
[[3]]
S4 class type : MassPeaks
Number of m/z values : 268
Range of m/z values : 2013.284 - 9954.596
Range of intensity values: 9.873e-05 - 6.992e-03
Range of snr values : 2.002 - 141.751
Memory usage : 15.898 KiB
Name : Pankreas_HB_L_061019_H7.O14
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid
[[4]]
S4 class type : MassPeaks
Number of m/z values : 265
Range of m/z values : 2018.063 - 9965.227
Range of intensity values: 9.431e-05 - 6.641e-03
Range of snr values : 2.007 - 141.312
Memory usage : 15.828 KiB
Name : Pankreas_HB_L_061019_H7.P13
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid
[[5]]
S4 class type : MassPeaks
Number of m/z values : 218
Range of m/z values : 2011.114 - 9717.072
Range of intensity values: 9.39e-05 - 6.213e-03
Range of snr values : 2.007 - 132.815
Memory usage : 14.727 KiB
Name : Pankreas_HB_L_061019_F10.L19
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid
[[6]]
S4 class type : MassPeaks
Number of m/z values : 249
Range of m/z values : 2002.301 - 9977.152
Range of intensity values: 9.989e-05 - 6.144e-03
Range of snr values : 2 - 123.044
Memory usage : 15.453 KiB
Name : Pankreas_HB_L_061019_F10.L20
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid
[[7]]
S4 class type : MassPeaks
Number of m/z values : 231
Range of m/z values : 2024.008 - 9954.596
Range of intensity values: 9.836e-05 - 5.975e-03
Range of snr values : 2.003 - 121.669
Memory usage : 15.031 KiB
Name : Pankreas_HB_L_061019_F9.L17
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid
[[8]]
S4 class type : MassPeaks
Number of m/z values : 221
Range of m/z values : 2020.672 - 9819.476
Range of intensity values: 9.469e-05 - 6.002e-03
Range of snr values : 2.001 - 126.825
Memory usage : 14.797 KiB
Name : Pankreas_HB_L_061019_F9.L18
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid
[[9]]
S4 class type : MassPeaks
Number of m/z values : 226
Range of m/z values : 2009.524 - 9928.206
Range of intensity values: 9.046e-05 - 6.703e-03
Range of snr values : 2.003 - 148.4
Memory usage : 14.922 KiB
Name : Pankreas_HB_L_061019_A6.A11
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid
[[10]]
S4 class type : MassPeaks
Number of m/z values : 232
Range of m/z values : 2020.672 - 9798.697
Range of intensity values: 8.948e-05 - 6.895e-03
Range of snr values : 2.001 - 154.204
Memory usage : 15.062 KiB
Name : Pankreas_HB_L_061019_A6.A12
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid
[[11]]
S4 class type : MassPeaks
Number of m/z values : 203
Range of m/z values : 2024.733 - 9987.795
Range of intensity values: 9.276e-05 - 5.557e-03
Range of snr values : 2.025 - 121.319
Memory usage : 14.383 KiB
Name : Pankreas_HB_L_061019_A8.A15
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid
[[12]]
S4 class type : MassPeaks
Number of m/z values : 205
Range of m/z values : 2008.945 - 9969.094
Range of intensity values: 8.707e-05 - 5.85e-03
Range of snr values : 2.011 - 135.137
Memory usage : 14.43 KiB
Name : Pankreas_HB_L_061019_A8.A16
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid
[[13]]
S4 class type : MassPeaks
Number of m/z values : 243
Range of m/z values : 2022.992 - 9977.152
Range of intensity values: 1.061e-04 - 4.145e-03
Range of snr values : 2.001 - 78.191
Memory usage : 15.32 KiB
Name : Pankreas_HB_L_061019_C4.F7
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid
[[14]]
S4 class type : MassPeaks
Number of m/z values : 220
Range of m/z values : 2012.416 - 9978.442
Range of intensity values: 1.029e-04 - 4.126e-03
Range of snr values : 2.009 - 80.584
Memory usage : 14.781 KiB
Name : Pankreas_HB_L_061019_C4.F8
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid
[[15]]
S4 class type : MassPeaks
Number of m/z values : 233
Range of m/z values : 2009.524 - 9958.139
Range of intensity values: 1.05e-04 - 4.285e-03
Range of snr values : 2 - 81.63
Memory usage : 15.086 KiB
Name : Pankreas_HB_L_061019_D9.G17
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid
[[16]]
S4 class type : MassPeaks
Number of m/z values : 249
Range of m/z values : 2007.355 - 9956.529
Range of intensity values: 1.026e-04 - 4.019e-03
Range of snr values : 2.004 - 78.473
Memory usage : 15.461 KiB
Name : Pankreas_HB_L_061019_D9.G18
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid
(def peaks-per-spectrum
(r->clj (r "sapply(all_peaks, length)")))peaks-per-spectrum[252 243 268 265 218 249 231 221 226 232 203 205 243 220 233 249]Step 3: Peak alignment
Peaks from different spectra may be slightly shifted in m/z due to instrument drift. alignSpectra uses a reference set of peaks to compute a warping function and applies it to the spectra.
(r "spectra_aligned <- alignSpectra(spectra, halfWindowSize=20, SNR=2)")[[1]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.224 - 10000.114
Range of intensity values: 0e+00 - 7.579e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
[[2]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.14 - 10001.921
Range of intensity values: 0e+00 - 7.353e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_G10.M20
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid
[[3]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.453 - 10001.949
Range of intensity values: 0e+00 - 6.992e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_H7.O14
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid
[[4]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2001.03 - 10005.194
Range of intensity values: 0e+00 - 6.641e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_H7.P13
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid
[[5]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1999.912 - 9998.049
Range of intensity values: 0e+00 - 6.213e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F10.L19
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid
[[6]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.215 - 9999.715
Range of intensity values: 0e+00 - 6.144e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F10.L20
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid
[[7]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1999.79 - 9997.317
Range of intensity values: 0e+00 - 5.975e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F9.L17
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid
[[8]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1999.792 - 9998.879
Range of intensity values: 0e+00 - 6.002e-03
Memory usage : 545 KiB
Name : Pankreas_HB_L_061019_F9.L18
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid
[[9]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.616 - 10002.042
Range of intensity values: 0e+00 - 6.703e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A6.A11
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid
[[10]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.727 - 10001.581
Range of intensity values: 0e+00 - 6.895e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A6.A12
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid
[[11]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.633 - 10001.254
Range of intensity values: 0e+00 - 5.557e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A8.A15
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid
[[12]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 2000.6 - 10000.147
Range of intensity values: 0e+00 - 5.85e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_A8.A16
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid
[[13]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1998.955 - 9994.75
Range of intensity values: 0e+00 - 4.145e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_C4.F7
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid
[[14]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1999.234 - 9995.479
Range of intensity values: 0e+00 - 4.126e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_C4.F8
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid
[[15]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1999.754 - 9996.686
Range of intensity values: 0e+00 - 4.285e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_D9.G17
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid
[[16]]
S4 class type : MassSpectrum
Number of m/z values : 34264
Range of m/z values : 1999.721 - 9999.414
Range of intensity values: 0e+00 - 4.019e-03
Memory usage : 545.008 KiB
Name : Pankreas_HB_L_061019_D9.G18
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid
(r "peaks_aligned <- detectPeaks(spectra_aligned, halfWindowSize=20, SNR=2, method='MAD')")[[1]]
S4 class type : MassPeaks
Number of m/z values : 252
Range of m/z values : 2012.214 - 9953.366
Range of intensity values: 9.657e-05 - 7.579e-03
Range of snr values : 2.003 - 157.225
Memory usage : 15.523 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
[[2]]
S4 class type : MassPeaks
Number of m/z values : 243
Range of m/z values : 2002.304 - 9862.327
Range of intensity values: 9.209e-05 - 7.353e-03
Range of snr values : 2.012 - 160.65
Memory usage : 15.312 KiB
Name : Pankreas_HB_L_061019_G10.M20
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid
[[3]]
S4 class type : MassPeaks
Number of m/z values : 268
Range of m/z values : 2013.601 - 9956.811
Range of intensity values: 9.873e-05 - 6.992e-03
Range of snr values : 2.002 - 141.751
Memory usage : 15.898 KiB
Name : Pankreas_HB_L_061019_H7.O14
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid
[[4]]
S4 class type : MassPeaks
Number of m/z values : 265
Range of m/z values : 2018.956 - 9970.686
Range of intensity values: 9.431e-05 - 6.641e-03
Range of snr values : 2.007 - 141.312
Memory usage : 15.828 KiB
Name : Pankreas_HB_L_061019_H7.P13
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid
[[5]]
S4 class type : MassPeaks
Number of m/z values : 218
Range of m/z values : 2010.89 - 9715.387
Range of intensity values: 9.39e-05 - 6.213e-03
Range of snr values : 2.007 - 132.815
Memory usage : 14.727 KiB
Name : Pankreas_HB_L_061019_F10.L19
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid
[[6]]
S4 class type : MassPeaks
Number of m/z values : 249
Range of m/z values : 2002.379 - 9977.133
Range of intensity values: 9.989e-05 - 6.144e-03
Range of snr values : 2 - 123.044
Memory usage : 15.453 KiB
Name : Pankreas_HB_L_061019_F10.L20
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid
[[7]]
S4 class type : MassPeaks
Number of m/z values : 231
Range of m/z values : 2023.662 - 9952.179
Range of intensity values: 9.836e-05 - 5.975e-03
Range of snr values : 2.003 - 121.669
Memory usage : 15.031 KiB
Name : Pankreas_HB_L_061019_F9.L17
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid
[[8]]
S4 class type : MassPeaks
Number of m/z values : 221
Range of m/z values : 2020.327 - 9818.621
Range of intensity values: 9.469e-05 - 6.002e-03
Range of snr values : 2.001 - 126.825
Memory usage : 14.797 KiB
Name : Pankreas_HB_L_061019_F9.L18
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid
[[9]]
S4 class type : MassPeaks
Number of m/z values : 226
Range of m/z values : 2010.002 - 9930.513
Range of intensity values: 9.046e-05 - 6.703e-03
Range of snr values : 2.003 - 148.4
Memory usage : 14.922 KiB
Name : Pankreas_HB_L_061019_A6.A11
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid
[[10]]
S4 class type : MassPeaks
Number of m/z values : 232
Range of m/z values : 2021.263 - 9800.543
Range of intensity values: 8.948e-05 - 6.895e-03
Range of snr values : 2.001 - 154.204
Memory usage : 15.062 KiB
Name : Pankreas_HB_L_061019_A6.A12
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid
[[11]]
S4 class type : MassPeaks
Number of m/z values : 203
Range of m/z values : 2025.23 - 9989.315
Range of intensity values: 9.276e-05 - 5.557e-03
Range of snr values : 2.025 - 121.319
Memory usage : 14.383 KiB
Name : Pankreas_HB_L_061019_A8.A15
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid
[[12]]
S4 class type : MassPeaks
Number of m/z values : 205
Range of m/z values : 2009.408 - 9969.506
Range of intensity values: 8.707e-05 - 5.85e-03
Range of snr values : 2.011 - 135.137
Memory usage : 14.43 KiB
Name : Pankreas_HB_L_061019_A8.A16
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid
[[13]]
S4 class type : MassPeaks
Number of m/z values : 243
Range of m/z values : 2021.81 - 9972.168
Range of intensity values: 1.061e-04 - 4.145e-03
Range of snr values : 2.001 - 78.191
Memory usage : 15.32 KiB
Name : Pankreas_HB_L_061019_C4.F7
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid
[[14]]
S4 class type : MassPeaks
Number of m/z values : 220
Range of m/z values : 2011.513 - 9974.187
Range of intensity values: 1.029e-04 - 4.126e-03
Range of snr values : 2.009 - 80.584
Memory usage : 14.781 KiB
Name : Pankreas_HB_L_061019_C4.F8
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid
[[15]]
S4 class type : MassPeaks
Number of m/z values : 233
Range of m/z values : 2009.141 - 9955.091
Range of intensity values: 1.05e-04 - 4.285e-03
Range of snr values : 2 - 81.63
Memory usage : 15.086 KiB
Name : Pankreas_HB_L_061019_D9.G17
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid
[[16]]
S4 class type : MassPeaks
Number of m/z values : 249
Range of m/z values : 2006.94 - 9956.209
Range of intensity values: 1.026e-04 - 4.019e-03
Range of snr values : 2.004 - 78.473
Memory usage : 15.461 KiB
Name : Pankreas_HB_L_061019_D9.G18
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid
Step 4: Peak binning
Even after alignment, exact m/z values differ slightly between spectra. binPeaks clusters nearby m/z values into shared bins.
(r "peaks_binned <- binPeaks(peaks_aligned)")[[1]]
S4 class type : MassPeaks
Number of m/z values : 252
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 9.657e-05 - 7.579e-03
Range of snr values : 2.003 - 157.225
Memory usage : 15.523 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
[[2]]
S4 class type : MassPeaks
Number of m/z values : 243
Range of m/z values : 2002.342 - 9868.06
Range of intensity values: 9.209e-05 - 7.353e-03
Range of snr values : 2.012 - 160.65
Memory usage : 15.312 KiB
Name : Pankreas_HB_L_061019_G10.M20
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid
[[3]]
S4 class type : MassPeaks
Number of m/z values : 268
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 9.873e-05 - 6.992e-03
Range of snr values : 2.002 - 141.751
Memory usage : 15.898 KiB
Name : Pankreas_HB_L_061019_H7.O14
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid
[[4]]
S4 class type : MassPeaks
Number of m/z values : 265
Range of m/z values : 2019.388 - 9973.725
Range of intensity values: 9.431e-05 - 6.641e-03
Range of snr values : 2.007 - 141.312
Memory usage : 15.828 KiB
Name : Pankreas_HB_L_061019_H7.P13
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid
[[5]]
S4 class type : MassPeaks
Number of m/z values : 218
Range of m/z values : 2010.464 - 9715.852
Range of intensity values: 9.39e-05 - 6.213e-03
Range of snr values : 2.007 - 132.815
Memory usage : 14.727 KiB
Name : Pankreas_HB_L_061019_F10.L19
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid
[[6]]
S4 class type : MassPeaks
Number of m/z values : 249
Range of m/z values : 2002.342 - 9973.725
Range of intensity values: 9.989e-05 - 6.144e-03
Range of snr values : 2 - 123.044
Memory usage : 15.453 KiB
Name : Pankreas_HB_L_061019_F10.L20
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid
[[7]]
S4 class type : MassPeaks
Number of m/z values : 231
Range of m/z values : 2023.298 - 9954.731
Range of intensity values: 9.836e-05 - 5.975e-03
Range of snr values : 2.003 - 121.669
Memory usage : 15.031 KiB
Name : Pankreas_HB_L_061019_F9.L17
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid
[[8]]
S4 class type : MassPeaks
Number of m/z values : 221
Range of m/z values : 2019.388 - 9816.199
Range of intensity values: 9.469e-05 - 6.002e-03
Range of snr values : 2.001 - 126.825
Memory usage : 14.797 KiB
Name : Pankreas_HB_L_061019_F9.L18
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid
[[9]]
S4 class type : MassPeaks
Number of m/z values : 226
Range of m/z values : 2010.464 - 9925.968
Range of intensity values: 9.046e-05 - 6.703e-03
Range of snr values : 2.003 - 148.4
Memory usage : 14.922 KiB
Name : Pankreas_HB_L_061019_A6.A11
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid
[[10]]
S4 class type : MassPeaks
Number of m/z values : 232
Range of m/z values : 2023.298 - 9796.211
Range of intensity values: 8.948e-05 - 6.895e-03
Range of snr values : 2.001 - 154.204
Memory usage : 15.062 KiB
Name : Pankreas_HB_L_061019_A6.A12
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid
[[11]]
S4 class type : MassPeaks
Number of m/z values : 203
Range of m/z values : 2023.298 - 9989.315
Range of intensity values: 9.276e-05 - 5.557e-03
Range of snr values : 2.025 - 121.319
Memory usage : 14.383 KiB
Name : Pankreas_HB_L_061019_A8.A15
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid
[[12]]
S4 class type : MassPeaks
Number of m/z values : 205
Range of m/z values : 2010.464 - 9973.725
Range of intensity values: 8.707e-05 - 5.85e-03
Range of snr values : 2.011 - 135.137
Memory usage : 14.43 KiB
Name : Pankreas_HB_L_061019_A8.A16
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid
[[13]]
S4 class type : MassPeaks
Number of m/z values : 243
Range of m/z values : 2023.298 - 9973.725
Range of intensity values: 1.061e-04 - 4.145e-03
Range of snr values : 2.001 - 78.191
Memory usage : 15.32 KiB
Name : Pankreas_HB_L_061019_C4.F7
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid
[[14]]
S4 class type : MassPeaks
Number of m/z values : 220
Range of m/z values : 2010.464 - 9973.725
Range of intensity values: 1.029e-04 - 4.126e-03
Range of snr values : 2.009 - 80.584
Memory usage : 14.781 KiB
Name : Pankreas_HB_L_061019_C4.F8
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid
[[15]]
S4 class type : MassPeaks
Number of m/z values : 233
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 1.05e-04 - 4.285e-03
Range of snr values : 2 - 81.63
Memory usage : 15.086 KiB
Name : Pankreas_HB_L_061019_D9.G17
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid
[[16]]
S4 class type : MassPeaks
Number of m/z values : 249
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 1.026e-04 - 4.019e-03
Range of snr values : 2.004 - 78.473
Memory usage : 15.461 KiB
Name : Pankreas_HB_L_061019_D9.G18
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid
Step 5: Peak filtering
filterPeaks keeps only peaks that appear in at least a minimum fraction of spectra. With minFrequency=0.25, a peak must appear in at least 4 of 16 spectra.
(r "peaks_filtered <- filterPeaks(peaks_binned, minFrequency=0.25)")[[1]]
S4 class type : MassPeaks
Number of m/z values : 225
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 9.711e-05 - 7.579e-03
Range of snr values : 2.014 - 157.225
Memory usage : 14.891 KiB
Name : Pankreas_HB_L_061019_G10.M19
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m19/1/1SLin/fid
[[2]]
S4 class type : MassPeaks
Number of m/z values : 218
Range of m/z values : 2023.298 - 9868.06
Range of intensity values: 9.209e-05 - 7.353e-03
Range of snr values : 2.012 - 160.65
Memory usage : 14.727 KiB
Name : Pankreas_HB_L_061019_G10.M20
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_G10/0_m20/1/1SLin/fid
[[3]]
S4 class type : MassPeaks
Number of m/z values : 233
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 9.873e-05 - 6.992e-03
Range of snr values : 2.002 - 141.751
Memory usage : 15.078 KiB
Name : Pankreas_HB_L_061019_H7.O14
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_o14/1/1SLin/fid
[[4]]
S4 class type : MassPeaks
Number of m/z values : 230
Range of m/z values : 2019.388 - 9973.725
Range of intensity values: 9.431e-05 - 6.641e-03
Range of snr values : 2.007 - 141.312
Memory usage : 15.008 KiB
Name : Pankreas_HB_L_061019_H7.P13
File : /data/set A - discovery leipzig/control/Pankreas_HB_L_061019_H7/0_p13/1/1SLin/fid
[[5]]
S4 class type : MassPeaks
Number of m/z values : 205
Range of m/z values : 2010.464 - 9715.852
Range of intensity values: 9.39e-05 - 6.213e-03
Range of snr values : 2.007 - 132.815
Memory usage : 14.422 KiB
Name : Pankreas_HB_L_061019_F10.L19
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l19/1/1SLin/fid
[[6]]
S4 class type : MassPeaks
Number of m/z values : 210
Range of m/z values : 2023.298 - 9973.725
Range of intensity values: 9.989e-05 - 6.144e-03
Range of snr values : 2 - 123.044
Memory usage : 14.539 KiB
Name : Pankreas_HB_L_061019_F10.L20
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F10/0_l20/1/1SLin/fid
[[7]]
S4 class type : MassPeaks
Number of m/z values : 213
Range of m/z values : 2023.298 - 9954.731
Range of intensity values: 9.836e-05 - 5.975e-03
Range of snr values : 2.003 - 121.669
Memory usage : 14.609 KiB
Name : Pankreas_HB_L_061019_F9.L17
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l17/1/1SLin/fid
[[8]]
S4 class type : MassPeaks
Number of m/z values : 205
Range of m/z values : 2019.388 - 9816.199
Range of intensity values: 9.469e-05 - 6.002e-03
Range of snr values : 2.001 - 126.825
Memory usage : 14.422 KiB
Name : Pankreas_HB_L_061019_F9.L18
File : /data/set A - discovery leipzig/tumor/Pankreas_HB_L_061019_F9/0_l18/1/1SLin/fid
[[9]]
S4 class type : MassPeaks
Number of m/z values : 208
Range of m/z values : 2010.464 - 9925.968
Range of intensity values: 9.046e-05 - 6.703e-03
Range of snr values : 2.003 - 148.4
Memory usage : 14.5 KiB
Name : Pankreas_HB_L_061019_A6.A11
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a11/1/1SLin/fid
[[10]]
S4 class type : MassPeaks
Number of m/z values : 214
Range of m/z values : 2023.298 - 9758.985
Range of intensity values: 8.948e-05 - 6.895e-03
Range of snr values : 2.001 - 154.204
Memory usage : 14.641 KiB
Name : Pankreas_HB_L_061019_A6.A12
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A6/0_a12/1/1SLin/fid
[[11]]
S4 class type : MassPeaks
Number of m/z values : 194
Range of m/z values : 2023.298 - 9973.725
Range of intensity values: 9.276e-05 - 5.557e-03
Range of snr values : 2.025 - 121.319
Memory usage : 14.172 KiB
Name : Pankreas_HB_L_061019_A8.A15
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a15/1/1SLin/fid
[[12]]
S4 class type : MassPeaks
Number of m/z values : 194
Range of m/z values : 2010.464 - 9973.725
Range of intensity values: 8.707e-05 - 5.85e-03
Range of snr values : 2.011 - 135.137
Memory usage : 14.172 KiB
Name : Pankreas_HB_L_061019_A8.A16
File : /data/set B - discovery heidelberg/control/Pankreas_HB_L_061019_A8/0_a16/1/1SLin/fid
[[13]]
S4 class type : MassPeaks
Number of m/z values : 214
Range of m/z values : 2023.298 - 9973.725
Range of intensity values: 1.061e-04 - 4.145e-03
Range of snr values : 2.001 - 78.191
Memory usage : 14.641 KiB
Name : Pankreas_HB_L_061019_C4.F7
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f7/1/1SLin/fid
[[14]]
S4 class type : MassPeaks
Number of m/z values : 195
Range of m/z values : 2010.464 - 9973.725
Range of intensity values: 1.03e-04 - 4.126e-03
Range of snr values : 2.011 - 80.584
Memory usage : 14.195 KiB
Name : Pankreas_HB_L_061019_C4.F8
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_C4/0_f8/1/1SLin/fid
[[15]]
S4 class type : MassPeaks
Number of m/z values : 207
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 1.052e-04 - 4.285e-03
Range of snr values : 2.004 - 81.63
Memory usage : 14.477 KiB
Name : Pankreas_HB_L_061019_D9.G17
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g17/1/1SLin/fid
[[16]]
S4 class type : MassPeaks
Number of m/z values : 213
Range of m/z values : 2010.464 - 9954.731
Range of intensity values: 1.026e-04 - 4.019e-03
Range of snr values : 2.004 - 78.473
Memory usage : 14.617 KiB
Name : Pankreas_HB_L_061019_D9.G18
File : /data/set B - discovery heidelberg/tumor/Pankreas_HB_L_061019_D9/0_g18/1/1SLin/fid
(def n-filtered-peaks
(r->clj (r "sapply(peaks_filtered, length)")))n-filtered-peaks[225 218 233 230 205 210 213 205 208 214 194 194 214 195 207 213]Step 6: Feature matrix
intensityMatrix converts the aligned, binned, filtered peaks into a samples-by-features matrix suitable for machine learning.
(r "fm <- intensityMatrix(peaks_filtered, spectra_aligned)") 2010.46372181388 2019.38802650132 2023.2977876444 2038.72956667587
[1,] 1.210506e-04 1.993417e-04 1.070342e-04 7.300137e-05
[2,] 4.400536e-05 3.790488e-05 1.025702e-04 1.047463e-04
[3,] 1.155278e-04 1.448812e-04 2.626509e-05 9.281477e-05
[4,] 3.132117e-05 1.544475e-04 6.939479e-05 7.105812e-05
[5,] 1.044336e-04 1.630882e-05 2.115012e-04 2.371837e-05
[6,] 2.504093e-05 6.697287e-05 1.941454e-04 5.363917e-05
[7,] 7.886063e-05 6.570303e-05 1.825488e-04 9.492398e-05
[8,] 3.341655e-05 1.394128e-04 1.247749e-04 4.045832e-05
[9,] 1.074566e-04 6.510684e-05 1.265661e-04 5.672352e-05
[10,] 6.208333e-05 9.906698e-05 1.228416e-04 7.211646e-05
[11,] 4.089187e-05 9.318478e-05 2.124132e-04 1.422758e-04
[12,] 9.587934e-05 8.995848e-05 1.950347e-04 1.056014e-04
[13,] 9.775870e-06 3.692000e-04 8.278236e-04 2.269902e-04
[14,] 1.202038e-04 3.645247e-04 8.898072e-04 1.527356e-04
[15,] 1.067410e-04 1.903003e-04 7.910257e-04 1.263589e-04
[16,] 2.563730e-04 2.718498e-04 7.406616e-04 1.256374e-04
2045.65282117107 2067.61159972805 2072.04781721356 2081.62304745686
[1,] 0.0001342010 0.0001425297 8.445436e-05 0.0005918102
[2,] 0.0001402854 0.0002319625 1.721385e-04 0.0006515445
[3,] 0.0001099131 0.0001758044 1.085525e-04 0.0008590112
[4,] 0.0001621597 0.0001824497 1.082504e-04 0.0009218033
[5,] 0.0002368342 0.0002051817 1.821955e-04 0.0006923273
[6,] 0.0001907535 0.0001579290 2.161255e-04 0.0007315509
[7,] 0.0001876065 0.0001862506 8.549708e-05 0.0004805097
[8,] 0.0001601275 0.0002114925 9.081995e-05 0.0004360625
[9,] 0.0002233786 0.0001618136 1.179099e-04 0.0003716667
[10,] 0.0002480737 0.0001736907 1.562085e-04 0.0003607110
[11,] 0.0002183129 0.0001794301 1.368684e-04 0.0008051578
[12,] 0.0002086279 0.0001439165 1.509857e-04 0.0007614646
[13,] 0.0001823328 0.0002658753 9.440444e-05 0.0014384219
[14,] 0.0002556911 0.0002067906 3.187510e-05 0.0016660713
[15,] 0.0001630247 0.0002604932 4.044431e-05 0.0023278542
[16,] 0.0002095761 0.0002488383 7.037197e-05 0.0019315328
2092.4017847307 2105.13340864733 2113.53888094399 2123.28263737811
[1,] 1.185319e-04 0.0004186724 1.628411e-05 9.859979e-05
[2,] 2.042644e-04 0.0004713007 1.086596e-04 6.004790e-05
[3,] 8.327090e-05 0.0005463139 6.833207e-05 6.850584e-05
[4,] 7.617156e-05 0.0005623556 1.275649e-04 2.613654e-05
[5,] 3.738036e-04 0.0007856701 1.734118e-04 3.550277e-05
[6,] 3.497580e-04 0.0007212871 2.574773e-04 6.003622e-05
[7,] 2.668241e-04 0.0003932749 1.183426e-04 1.953994e-05
[8,] 1.604252e-04 0.0005785555 1.776502e-04 4.870442e-05
[9,] 1.794671e-04 0.0007017110 1.006928e-04 7.668267e-05
[10,] 1.024838e-04 0.0007434170 9.958325e-05 6.163105e-05
[11,] 1.862946e-04 0.0008241476 1.617020e-04 4.131826e-05
[12,] 3.194351e-04 0.0007634470 1.438166e-04 8.794021e-05
[13,] 4.503198e-04 0.0005155775 2.353579e-05 1.549241e-04
[14,] 6.458137e-04 0.0006397791 3.365175e-05 7.578327e-05
[15,] 6.579865e-04 0.0004945284 1.904985e-04 1.854927e-04
[16,] 3.212661e-04 0.0004231703 1.533510e-04 7.832647e-05
2134.16642829054 2141.35288165096 2153.28194753832 2159.37044610478
[1,] 4.726874e-05 1.839750e-04 1.124081e-04 1.379477e-04
[2,] 2.361132e-05 1.031389e-04 1.400458e-04 1.138354e-04
[3,] 5.414960e-05 7.138999e-05 1.215775e-04 1.209412e-04
[4,] 7.707720e-05 5.468827e-05 1.373768e-04 1.389748e-04
[5,] 1.642870e-04 4.204271e-05 9.377908e-05 4.054494e-04
[6,] 1.274355e-04 7.631858e-05 3.387959e-05 4.567983e-04
[7,] 1.319369e-04 9.896772e-05 1.453400e-04 1.525286e-04
[8,] 1.213553e-04 1.051518e-04 1.644955e-04 1.222403e-04
[9,] 2.078657e-04 1.432580e-04 1.987542e-04 1.610447e-04
[10,] 1.302583e-04 4.216021e-05 1.283282e-04 9.673127e-05
[11,] 1.192442e-04 7.995527e-05 6.898373e-04 1.667249e-04
[12,] 1.209645e-04 4.580054e-05 6.300736e-04 2.445718e-04
[13,] 1.796098e-04 1.483155e-04 1.355487e-04 7.561801e-05
[14,] 1.531785e-04 1.917656e-04 2.318144e-04 1.730311e-04
[15,] 1.725470e-04 3.863328e-05 5.249275e-04 6.606523e-05
[16,] 1.799566e-04 1.118773e-04 3.680441e-04 4.797371e-05
2163.25287420978 2178.82247406275 2190.67003646009 2194.26201501391
[1,] 1.502802e-04 1.863214e-05 2.594915e-04 1.911162e-04
[2,] 1.689144e-04 1.223341e-04 2.195439e-04 1.644015e-04
[3,] 1.301144e-04 1.720309e-05 7.482642e-05 5.419167e-05
[4,] 1.574197e-04 9.869539e-05 1.636902e-04 1.001798e-04
[5,] 3.431557e-04 1.400267e-04 2.046047e-04 1.594414e-04
[6,] 3.449122e-04 1.264888e-04 3.206671e-04 2.012030e-04
[7,] 1.821983e-04 1.180233e-04 1.169750e-04 1.497595e-04
[8,] 1.692560e-04 8.661295e-05 1.373337e-04 1.266002e-04
[9,] 1.291682e-04 1.422056e-04 7.360140e-05 1.968361e-05
[10,] 1.014572e-04 1.290877e-04 9.730383e-05 8.839511e-06
[11,] 1.592804e-04 1.408048e-04 1.784765e-04 6.904852e-05
[12,] 2.506036e-04 1.767715e-04 2.185821e-04 1.436901e-04
[13,] 1.038445e-04 3.549528e-04 1.773862e-04 2.008118e-04
[14,] 4.514342e-05 3.685949e-04 1.277698e-04 1.952820e-04
[15,] 1.621268e-04 1.189537e-04 6.529312e-05 1.010653e-04
[16,] 6.842879e-05 1.080535e-04 1.013197e-04 3.495206e-05
2209.90566739532 2230.59383637624 2245.13341811979 2251.27533270642
[1,] 0.0005026185 1.133986e-04 1.172736e-04 1.371885e-04
[2,] 0.0005730879 7.728257e-06 1.139034e-04 1.420245e-04
[3,] 0.0005817462 3.257954e-05 1.078990e-04 1.275623e-04
[4,] 0.0007156735 9.932051e-05 1.138395e-04 2.433278e-05
[5,] 0.0003700478 4.589567e-06 9.613422e-05 1.483900e-04
[6,] 0.0003360071 4.537446e-05 1.772963e-04 1.227221e-04
[7,] 0.0001671910 1.502636e-04 1.292791e-05 8.084299e-05
[8,] 0.0001847546 1.213602e-04 1.545467e-05 7.416765e-05
[9,] 0.0001886906 2.951223e-05 9.450751e-05 1.610857e-04
[10,] 0.0001576984 1.022401e-04 9.150112e-05 1.472656e-04
[11,] 0.0003855563 6.512682e-05 1.220892e-04 1.246931e-04
[12,] 0.0004315023 1.076251e-04 1.556182e-04 1.553644e-04
[13,] 0.0008125446 2.838138e-04 2.277801e-04 2.280742e-04
[14,] 0.0010096752 4.136386e-04 2.810983e-04 2.153144e-04
[15,] 0.0013348338 2.183419e-04 4.598612e-05 2.766289e-04
[16,] 0.0010992321 2.665814e-04 5.787841e-06 2.082191e-04
2264.90793102928 2279.20283071085 2294.35901377343 2306.622848006
[1,] 1.829270e-04 2.457157e-04 0.0004374749 1.243566e-04
[2,] 2.092193e-04 2.283668e-04 0.0004924751 6.211185e-05
[3,] 1.454510e-04 1.942717e-04 0.0002252753 1.214029e-04
[4,] 1.417238e-04 2.542556e-04 0.0003357565 1.135370e-04
[5,] 1.505699e-04 3.238407e-04 0.0002605278 1.097341e-04
[6,] 1.779764e-04 2.760804e-04 0.0003215382 6.530919e-05
[7,] 4.823964e-05 2.601626e-04 0.0004651447 6.546152e-05
[8,] 9.540997e-05 2.327038e-04 0.0003345341 4.937287e-05
[9,] 5.419122e-05 2.315878e-04 0.0003199438 6.215578e-05
[10,] 5.824273e-05 3.594388e-04 0.0002817886 1.003158e-04
[11,] 5.602852e-05 3.368095e-04 0.0002992864 1.031659e-04
[12,] 8.904675e-05 3.009937e-04 0.0003458662 4.789239e-05
[13,] 1.956681e-04 1.934717e-04 0.0002218202 1.516982e-04
[14,] 1.177938e-04 2.502679e-04 0.0002060572 1.516835e-04
[15,] 2.225413e-04 8.721711e-05 0.0003775174 2.190758e-05
[16,] 1.375694e-04 5.988392e-05 0.0003663471 2.254469e-05
2318.54348347902 2325.93176963302 2337.12821512602 2347.7175129187
[1,] 1.238909e-04 2.138919e-04 1.166121e-04 0.0001706054
[2,] 6.808896e-05 2.742421e-04 1.019963e-04 0.0001599298
[3,] 1.228191e-04 1.557572e-04 7.142836e-05 0.0001861974
[4,] 4.608879e-05 2.193549e-04 1.745118e-04 0.0001796775
[5,] 1.080953e-04 2.619737e-04 1.293430e-04 0.0005923731
[6,] 1.939910e-05 2.565609e-04 9.988878e-05 0.0006462369
[7,] 3.517646e-05 2.028612e-04 1.293507e-04 0.0003095121
[8,] 9.925096e-05 1.267505e-04 1.366139e-04 0.0001898630
[9,] 7.105093e-05 1.356901e-04 1.080640e-04 0.0002098793
[10,] 4.811016e-05 1.761726e-04 1.463797e-04 0.0001935491
[11,] 1.187857e-04 2.133390e-04 8.071830e-05 0.0003500119
[12,] 5.119687e-05 1.483440e-04 9.062143e-05 0.0004387959
[13,] 9.525553e-05 1.727064e-04 1.622828e-04 0.0002118830
[14,] 6.049727e-05 1.803115e-04 1.441695e-04 0.0001804813
[15,] 3.650622e-05 7.288604e-05 1.372503e-04 0.0002041231
[16,] 8.021492e-05 1.493321e-04 1.105451e-04 0.0002046691
2354.24766595096 2368.9430574178 2379.27591342701 2393.05103731591
[1,] 1.192660e-04 1.091742e-04 0.0001888534 1.130613e-04
[2,] 7.583024e-05 1.205953e-04 0.0001475808 5.027920e-05
[3,] 1.512519e-04 1.188988e-04 0.0002159035 1.071039e-04
[4,] 1.062182e-04 3.567815e-05 0.0002092932 4.308708e-05
[5,] 3.529362e-04 1.849871e-04 0.0001687255 2.065127e-05
[6,] 2.378844e-04 2.097522e-04 0.0001975256 6.666997e-05
[7,] 1.856675e-04 1.846877e-04 0.0001474264 3.221204e-05
[8,] 1.597400e-04 1.020625e-04 0.0001808097 6.353401e-05
[9,] 8.770636e-05 4.546645e-05 0.0003056160 4.454428e-05
[10,] 6.079276e-05 3.021889e-05 0.0003084305 3.154424e-05
[11,] 1.688449e-04 1.817090e-05 0.0003045908 5.766195e-05
[12,] 1.004627e-04 1.942487e-05 0.0002807963 1.441520e-05
[13,] 1.115136e-04 1.259230e-04 0.0002768048 6.396481e-05
[14,] 6.962496e-05 1.452142e-05 0.0002534977 1.055760e-04
[15,] 2.427989e-04 1.152666e-04 0.0003018159 1.365914e-04
[16,] 2.096202e-04 3.320767e-05 0.0002961587 1.490199e-04
2403.46795853612 2409.22571493166 2423.58654051572 2428.26413301708
[1,] 1.577363e-05 5.954957e-05 0.0003329138 0.0001162420
[2,] 5.268437e-05 1.110753e-04 0.0003983258 0.0002016261
[3,] 5.258884e-05 1.094004e-04 0.0002584966 0.0002135025
[4,] 8.332537e-05 1.405406e-04 0.0002801275 0.0001235750
[5,] 3.236710e-05 6.058568e-05 0.0008880456 0.0002970524
[6,] 1.219210e-04 1.181719e-04 0.0007940647 0.0002802373
[7,] 1.034128e-04 7.019435e-05 0.0005659396 0.0002735074
[8,] 1.035426e-04 1.042858e-04 0.0005382558 0.0002139753
[9,] 1.347162e-04 1.032616e-04 0.0005838508 0.0002144275
[10,] 9.014908e-05 9.271911e-05 0.0004796576 0.0002228970
[11,] 1.044312e-04 3.727586e-05 0.0010702982 0.0003735978
[12,] 8.807097e-05 1.052361e-04 0.0011106388 0.0003948748
[13,] 6.639507e-05 1.905727e-04 0.0002338446 0.0005767909
[14,] 6.870946e-05 1.185889e-04 0.0003232034 0.0005955444
[15,] 1.391586e-05 9.403466e-05 0.0003855334 0.0002736294
[16,] 7.051330e-05 1.727922e-04 0.0002954989 0.0003036939
2449.52823053379 2467.0020493968 2481.94695020369 2495.00406132144
[1,] 1.741170e-04 0.0002245977 1.231931e-04 0.0003557956
[2,] 1.478056e-04 0.0002737704 6.956824e-05 0.0004749649
[3,] 1.376724e-04 0.0003369703 9.498596e-06 0.0003419785
[4,] 1.516775e-04 0.0003534002 7.201056e-05 0.0003743264
[5,] 1.596141e-04 0.0001532583 1.451102e-04 0.0014182648
[6,] 1.251367e-04 0.0001684937 5.022206e-05 0.0014322568
[7,] 8.287858e-05 0.0003500193 1.583734e-04 0.0005858222
[8,] 1.937461e-04 0.0003210217 1.065091e-04 0.0005766024
[9,] 1.234161e-04 0.0004939895 3.610891e-05 0.0006040369
[10,] 1.705453e-04 0.0004344638 3.539286e-05 0.0005652330
[11,] 9.311752e-05 0.0003451684 4.440599e-05 0.0011138608
[12,] 1.677007e-04 0.0003131997 7.342917e-05 0.0012423658
[13,] 8.239925e-05 0.0002619775 3.452373e-05 0.0003628592
[14,] 3.494458e-05 0.0002890333 1.475881e-06 0.0003364380
[15,] 1.102017e-04 0.0007833182 1.108998e-04 0.0001663123
[16,] 6.243737e-05 0.0006928464 1.199072e-04 0.0001793832
2509.80866216721 2522.31009107036 2535.61788550317 2545.10431985288
[1,] 0.0002341934 1.262669e-04 1.074606e-04 1.467599e-04
[2,] 0.0002272636 9.983892e-05 1.038475e-04 1.317387e-04
[3,] 0.0001753728 1.282657e-04 1.209328e-04 8.850545e-05
[4,] 0.0002231120 1.456878e-04 2.685878e-06 1.432198e-04
[5,] 0.0004603191 3.626883e-05 5.409371e-05 1.466076e-04
[6,] 0.0003343744 1.081736e-04 6.740275e-05 1.157324e-04
[7,] 0.0002777326 1.214569e-04 1.077940e-04 1.584884e-04
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[7,] 1.025027e-04 6.626735e-05 1.451279e-04 9.513360e-05
[8,] 1.866566e-05 4.526266e-05 6.601159e-05 5.462779e-05
[9,] 7.994335e-06 9.199696e-05 1.253754e-05 4.112972e-05
[10,] 5.602521e-05 1.825694e-05 3.643667e-05 2.247582e-05
[11,] 4.681403e-05 1.681284e-05 3.646940e-05 9.619929e-05
[12,] 3.403309e-05 5.396253e-05 3.627615e-05 8.706792e-05
[13,] 1.087972e-04 1.227843e-04 5.098598e-05 1.204490e-04
[14,] 7.184304e-05 1.978984e-05 5.369319e-05 1.037623e-04
[15,] 2.761308e-05 1.065435e-04 1.216641e-04 2.497984e-05
[16,] 3.127558e-06 3.814242e-05 1.048949e-04 7.129167e-07
attr(,"mass")
[1] 2010.464 2019.388 2023.298 2038.730 2045.653 2067.612 2072.048 2081.623
[9] 2092.402 2105.133 2113.539 2123.283 2134.166 2141.353 2153.282 2159.370
[17] 2163.253 2178.822 2190.670 2194.262 2209.906 2230.594 2245.133 2251.275
[25] 2264.908 2279.203 2294.359 2306.623 2318.543 2325.932 2337.128 2347.718
[33] 2354.248 2368.943 2379.276 2393.051 2403.468 2409.226 2423.587 2428.264
[41] 2449.528 2467.002 2481.947 2495.004 2509.809 2522.310 2535.618 2545.104
[49] 2553.945 2562.811 2581.172 2588.179 2604.235 2610.983 2616.838 2623.806
[57] 2632.543 2643.166 2660.077 2672.767 2682.197 2686.813 2698.685 2709.039
[65] 2714.062 2723.839 2730.790 2739.437 2754.069 2769.294 2789.914 2808.203
[73] 2819.463 2830.953 2845.176 2862.365 2876.960 2887.747 2902.462 2915.283
[81] 2932.338 2952.548 2972.578 2978.517 2990.574 3002.094 3016.728 3035.637
[89] 3045.087 3059.820 3075.786 3087.670 3096.109 3104.492 3117.843 3143.326
[97] 3158.628 3175.408 3191.721 3207.901 3217.086 3231.970 3240.807 3262.802
[105] 3279.245 3294.336 3303.236 3316.028 3325.276 3334.412 3365.637 3377.660
[113] 3408.431 3413.847 3419.966 3434.408 3448.202 3466.120 3489.130 3506.147
[121] 3524.497 3540.243 3568.710 3585.148 3605.547 3625.180 3634.955 3676.100
[129] 3680.957 3704.580 3719.562 3734.741 3744.047 3763.760 3768.644 3782.783
[137] 3795.357 3816.792 3860.968 3874.162 3882.934 3903.288 3909.626 3918.984
[145] 3934.213 3952.561 3961.831 3993.468 4019.242 4036.899 4053.877 4063.528
[153] 4071.561 4091.283 4110.141 4123.034 4145.672 4152.801 4166.886 4173.349
[161] 4192.541 4209.963 4235.389 4249.606 4266.145 4301.885 4337.888 4354.649
[169] 4363.025 4382.479 4397.039 4416.710 4430.783 4452.028 4466.989 4493.822
[177] 4530.408 4567.345 4586.415 4599.518 4613.850 4644.421 4663.772 4671.410
[185] 4696.965 4711.601 4717.148 4738.660 4756.701 4787.358 4818.734 4858.583
[193] 4889.085 4915.919 4929.085 4963.956 5003.961 5025.244 5045.645 5113.138
[201] 5131.497 5159.755 5204.149 5224.976 5248.491 5265.254 5292.677 5320.125
[209] 5336.945 5376.670 5391.092 5438.423 5463.825 5481.721 5507.572 5523.070
[217] 5549.992 5592.824 5631.538 5664.267 5709.068 5754.391 5805.847 5861.036
[225] 5888.020 5904.842 5944.594 5958.676 6004.039 6049.858 6075.112 6090.333
[233] 6142.796 6175.078 6191.473 6226.721 6271.807 6305.281 6332.679 6357.332
[241] 6378.453 6389.361 6433.139 6486.534 6492.818 6518.512 6561.920 6590.744
[249] 6614.658 6631.487 6669.480 6685.712 6749.089 6805.511 6831.844 6852.739
[257] 6909.415 6961.473 7008.657 7068.143 7131.327 7163.242 7191.426 7222.085
[265] 7291.270 7307.412 7343.962 7399.452 7432.803 7471.773 7550.614 7565.972
[273] 7636.797 7721.884 7766.712 7806.772 7820.654 7836.691 7875.971 7909.148
[281] 7924.860 8038.513 8092.124 8129.587 8143.627 8194.456 8217.087 8262.104
[289] 8301.565 8364.230 8429.664 8452.853 8500.583 8534.326 8566.378 8604.219
[297] 8657.569 8663.534 8677.052 8737.822 8757.217 8767.256 8810.002 8864.011
[305] 8935.253 8989.097 9062.593 9131.459 9136.944 9176.137 9290.928 9345.100
[313] 9425.915 9438.437 9478.958 9525.016 9590.430 9629.079 9715.852 9724.358
[321] 9758.985 9778.589 9816.199 9868.060 9885.321 9925.968 9954.731 9973.725
(def fm-dims (r->clj (r "dim(fm)")))fm-dims[16 328]The feature matrix has 16 rows (one per spectrum) and hundreds of columns (one per shared peak position).
(let [col-masses (r->clj (r "as.numeric(colnames(fm))"))
n-cols (count col-masses)]
{:n-samples (first fm-dims)
:n-features (second fm-dims)
:mass-range [(first col-masses) (last col-masses)]}){:n-samples 16,
:n-features 328,
:mass-range [2010.46372181388 9973.72548001882]}Summary
ClojisR makes it straightforward to call MALDIquant from Clojure. The key patterns are:
(r ...)with backtick-quoted forms and tilde splicing(r->clj ...)to bring R results back to Clojure vectors- R string expressions for complex nested calls
For multi-sample workflows (alignment, binning, feature matrices), MALDIquant can be called directly via ClojisR as shown above.
| MALDIquant function | Purpose | Key parameters |
|---|---|---|
| createMassSpectrum | Create spectrum object | mass, intensity |
| trim | Restrict mass range | range |
| transformIntensity | Variance stabilization | method (“sqrt”) |
| smoothIntensity | Noise reduction | method, halfWindowSize |
| removeBaseline | Background subtraction | method (“SNIP”), iterations |
| calibrateIntensity | Area normalization | method (“TIC”) |
| detectPeaks | Find peaks | halfWindowSize, SNR, method |
| alignSpectra | Correct m/z drift | halfWindowSize, SNR |
| binPeaks | Cluster peaks across spectra | (tolerance) |
| filterPeaks | Remove infrequent peaks | minFrequency |
| intensityMatrix | Build sample x feature matrix | peaks, spectra |