summarySpectra.RdThis function generates a numerical summary of a collection of MassSpectrum objects.
summarySpectra(x, digits = 4)A list of MassSpectrum objects.
Integer indicating the number of decimal places to be used.
For each MassSpectrum on the list this function provides summary statistics of m/z points and signal intensities (number, minimum, mean, standard deviation, median, mean absolute deviation, maximum).
A data.frame containing summary information of a collection of MassSpectrum objects.
# Load example data
data(spectra) # list of MassSpectra class objects
data(type) # metadata
# Summary of spectra features (results for 20 first mass spectra)
summarySpectra(spectra[1:20])
#> ID No.MZ Min.MZ Max.MZ Min.Int Mean.Int Std.Int Med.Int
#> 1 160408F21 1857 2500.05 12995.77 19 722.2649 572.9375 664
#> 2 160408F22 1857 2500.05 12995.77 18 637.1357 531.1853 582
#> 3 160408F23 1857 2500.05 12995.77 8 542.4976 447.7237 483
#> 4 160408F24 1857 2500.05 12995.77 34 957.3430 737.8402 903
#> 5 160408G01 1857 2500.05 12995.77 42 1129.8185 871.5639 1064
#> 6 160408G02 1857 2500.05 12995.77 24 637.1648 530.9029 595
#> 7 160408G03 1857 2500.05 12995.77 12 505.9499 442.6567 466
#> 8 160408G04 1857 2500.05 12995.77 43 984.1179 754.5525 936
#> 9 160408G05 1857 2500.05 12995.77 27 906.9138 686.9536 854
#> 10 160408G06 1857 2500.05 12995.77 46 906.9133 689.0228 891
#> 11 160408G07 1857 2500.05 12995.77 9 383.5385 339.6962 352
#> 12 160408G08 1857 2500.05 12995.77 26 756.7415 582.2340 715
#> 13 160408G09 1857 2500.05 12995.77 14 580.6947 522.7782 524
#> 14 160408G10 1857 2500.05 12995.77 30 730.3985 578.6044 686
#> 15 160408G11 1857 2500.05 12995.77 26 771.9882 651.0067 712
#> 16 160408G12 1857 2500.05 12995.77 86 995.9386 639.7584 1000
#> 17 160408G13 1857 2500.05 12995.77 128 1894.1125 1228.2008 1887
#> 18 160408G14 1857 2500.05 12995.77 27 925.0722 739.1213 866
#> 19 160408G15 1857 2500.05 12995.77 46 728.0070 615.4929 680
#> 20 160408G16 1857 2500.05 12995.77 37 932.3393 703.2897 897
#> MAD.Int Max.Int
#> 1 486.2928 5888
#> 2 382.5108 6128
#> 3 401.7846 4713
#> 4 587.1096 7843
#> 5 652.3440 7860
#> 6 358.7892 5459
#> 7 298.0026 5198
#> 8 530.7708 7333
#> 9 558.9402 6068
#> 10 481.8450 7505
#> 11 237.2160 3444
#> 12 426.9888 5410
#> 13 343.9632 5480
#> 14 415.1280 5948
#> 15 441.8148 6724
#> 16 471.4668 6310
#> 17 944.4162 10911
#> 18 541.1490 7509
#> 19 373.6152 8147
#> 20 493.7058 7631
# Some pre-processing
sc.results <- screenSpectra(spectra, meta = type)
spectra <- sc.results$fspectra
type <- sc.results$fmeta
spectra <- transformIntensity(spectra, method = "sqrt")
spectra <- wavSmoothing(spectra)
spectra <- removeBaseline(spectra)
names(spectra) <- type$SpectID # spectra IDs are lost with removeBaseline()
# Summary of spectra features (results for positions 10 to 20)
summarySpectra(spectra[10:20])
#> ID No.MZ Min.MZ Max.MZ Min.Int Mean.Int Std.Int Med.Int MAD.Int
#> 1 160408G06 1857 2500.05 12995.77 0 9.4187 7.4519 8.8096 4.8588
#> 2 160408G07 1857 2500.05 12995.77 0 6.1664 5.5858 5.4212 3.9122
#> 3 160408G08 1857 2500.05 12995.77 0 8.2888 7.1684 6.8744 5.0418
#> 4 160408G09 1857 2500.05 12995.77 0 7.8635 7.1346 6.6714 4.8903
#> 5 160408G10 1857 2500.05 12995.77 0 8.5955 7.3257 7.1295 5.3704
#> 6 160408G11 1857 2500.05 12995.77 0 8.7352 7.9063 6.9191 5.3274
#> 7 160408G12 1857 2500.05 12995.77 0 8.6025 6.5432 8.0877 4.5442
#> 8 160408G13 1857 2500.05 12995.77 0 11.4564 9.3089 10.0140 6.6083
#> 9 160408G14 1857 2500.05 12995.77 0 9.4141 8.2514 8.1230 5.8925
#> 10 160408G15 1857 2500.05 12995.77 0 8.7202 7.4111 7.6813 4.7545
#> 11 160408G16 1857 2500.05 12995.77 0 9.4661 7.7870 8.1631 5.5819
#> Max.Int
#> 1 70.7444
#> 2 48.6307
#> 3 60.5929
#> 4 63.1512
#> 5 64.3077
#> 6 69.8553
#> 7 60.6308
#> 8 81.1536
#> 9 72.6329
#> 10 75.9089
#> 11 72.2888